bluuebunny/crossref_metadata_2025 huggingface dataset:
Acoustic impedance measurements of pulse tube refrigerators
Authors: Iwase Takashi , Biwa Tetsushi , Yazaki Taichi
Published: February 2010

Complex acoustic impedance is determined in a prototype refrigerator that can mimic orifice-type, inertance-type, and double inlet-type pulse tube refrigerators from simultaneous measurements of pressure and velocity oscillations at the cold end. The impedance measurements revealed the means by which the oscillatory flow condition in the basic pulse tube refrigerator is improved by additional components such as a valve and a tank. The working mechanism of pulse tube refrigerators is explained based on an electrical circuit analogy.
Quantum-level control in a III–V-based ferromagnetic-semiconductor heterostructure with a GaMnAs quantum well and double barriers
Authors: Ohya Shinobu , Muneta Iriya , Tanaka Masaaki
Published: February 2010

We investigate the spin-dependent tunneling properties in a three-terminal III–V-based ferromagnetic-semiconductor heterostructure with a 2.5 nm thick GaMnAs quantum well (QW) and double barriers. We successfully control the quantum levels and modulate the spin-dependent current with varying the voltage of the electrode connected to the GaMnAs QW. Our results will open up a new possibility for realizing three-terminal spin resonant-tunneling devices.
Study of the Au Schottky contact formation on oxygen plasma treated n-type SnO2 (101) thin films
Authors: Nagata Takahiro , Bierwagen Oliver , White Mark E. , Tsai Min-Ying , Speck James S.
Published: February 2010

As-grown and oxygen plasma treated n-type tin dioxide (SnO2) (101) thin films were investigated regarding the properties of Au contacts, surface structure, and band bending. The plasma treatment was performed in a conventional oxygen plasma cleaning system with maximum oxygen ion energies of 400 eV. Whereas the as-deposited SnO2 film formed non-Schottky contacts with Au, the oxygen plasma treated films formed Schottky contacts with Au. Capacitance-voltage and differential Hall measurements indicated the introduction of bulk electron traps up to several 100 nm below the surface due to the oxygen plasma treatment. Angle resolved x-ray photoelectron spectroscopy (AR-XPS) revealed a surface accumulation layer on the as-grown film that was absent after the plasma treatment. These measurements further revealed chemical differences between the as-deposited and the plasma treated SnO2 surfaces. All SnO2 films had Sn2+–O bonds. The AR-XPS Sn2+–O signal intensity increased after plasma treatment, indicating that the oxygen plasma damaged the SnO2 surface. Additionally, an O2 adlayer was formed due to the oxygen plasma treatment. The damaged layer due to oxygen ion bombardment, oxygen adsorption layer, and possibly bulk traps depleted the surface carriers which enabled the formation of a Schottky contact with Au.
Strain sensing with submicron Al–AlOx–Al tunnel junctions
Authors: Koppinen P. J. , Lievonen J. T. , Ahlskog M. , Maasilta I. J.
Published: February 2010

We demonstrate a local strain sensing method for nanostructures based on metallic Al tunnel junctions with AlOx barriers. The junctions were fabricated on top of a thin silicon nitride membrane, which was actuated with an atomic force microscope tip attached to a stiff cantilever. A large relative change in the tunneling resistance in response to the applied strain (gauge factor) was observed up to a value of 37. This facilitates local static strain variation measurements down to ∼10−7. This type of strain sensor could have applications in nanoelectromechanical systems used in displacement, force, and mass sensing, for example.
Excited states of PbF: A four-component relativistic study
Authors: Yamamoto Shigeyoshi , Tatewaki Hiroshi
Published: February 2010

The electronic states of lead monofluoride (PbF) are studied from the (Pb 6s)2 (F 2p-π)4 (F 2p-σ)2 (Pb 6p-π)1 X1 ground state up to the F state, using the four-component relativistic configuration interaction and Fock-space coupled-cluster singles and doubles methods. Difficulties arising from the valence-Rydberg mixing are overcome by using a flexible basis set including Rydberg-type diffuse functions and by large-scale correlation calculations. The excited states are successfully characterized with the help of computed transition dipole moments. The three lowest-lying states (X1, X2, and A) are confirmed to be valence states arising from the (Pb 6p) spinors. The B state is assigned to the lowest Rydberg state (Ω=1/2), represented by a single excitation from the (Pb 6p-π) spinor to the (F 3s) Rydberg spinor. Its calculated excitation energy (4.30 eV) is comparable to the observed one (4.42 eV). The C state is a multiconfigurational valence state whose dominant configuration is represented by (Pb 6s)2 (F 2p-π)4 (F 2p-σ)1 (Pb 6p-π)2. Its calculated excitation energy (4.71 eV) is in good agreement with experiment (4.72 eV). The remaining D, E, and F states are assigned as Rydberg states. The calculated ionization potential (7.44 eV) is also close to the value (7.55 eV) determined recently by multiphoton ionization experiments.
Nonlinear whistler instability driven by a beamlike distribution of resonant electrons
Authors: Lampe Martin , Joyce Glenn , Manheimer Wallace M. , Ganguli Gurudas
Published: February 2010

Theory and simulation are used to study the instability of a coherent whistler parallel-propagating in a simplified model radiation belt with a background of cold electrons, as well as a ring distribution of energetic electrons. A nonlinear instability is initiated at the location z+, where the electrons are cyclotron resonant with the wave, on the side of the equator (z=0) where the wave is propagating away from the equator. The instability propagates backward toward the equator, growing both spatially and temporally. As the instability develops, frequency falls in such a way as to keep the electrons nearly resonant with the waves over the entire region 0<z<z+. The instability causes a sharp drop in the pitch angle of the resonant electrons and eventually saturates with peak amplitude near the equator.
Highly selective separation of DNA fragments using optically directed transport
Authors: Braiman Avital , Rudakov Fedor , Thundat Thomas
Published: February 2010

We present a design that allows selective separation of biomolecules of a particular size without performing complete separation of the sample by size. By focusing a laser beam onto a photoelectrode in contact with an electrolyte medium, a highly localized and optically controlled photoelectrophoretic trap is created. Moving the light beam along the photoelectrode consequently moves the trap. We demonstrate that by manipulating the speed of the photoelectrophoretic trap biomolecules of a particular size can be selectively separated from the mixture. We achieve a qualitative agreement between our experimental results and numerical simulations.
Effect of dipole interaction on microwave assisted magnetization switching
Authors: Okamoto S. , Kikuchi N. , Kitakami O. , Igarashi M.
Published: February 2010

Microwave assisted switching (MAS) of magnetization has attracted much attention as an alternative technique for future ultrahigh density magnetic recording. In this study, to elucidate the effect of magnetostatic interparticle interaction on MAS, we have calculated the switching behavior for a row of three uniaxial magnetic particles as a simplest case. When a dc field is applied only to one particle of the row in an ac field, MAS selectively occurs in the particle and not in the neighboring particles. This behavior may be very effective to realize narrow track recording without adjacent track erasure problem by downsizing a dc field source below an ac source. It has been also found that when both ac and dc fields are applied to all the particles, coherent magnetization precession is cooperatively induced in all the particles due to dipole-dipole interaction among neighboring particles, resulting in significant reduction of the switching field. This coherent magnetization precession is not only effective to reduce the switching field but also to suppress the effect of magnetic anisotropy dispersion, suggesting the effectiveness of MAS in granular recording media.
Gauge invariance and classical dynamics of noncommutative particle theory
Authors: Gitman D. M. , Kupriyanov V. G.
Published: February 2010

We consider a model of classical noncommutative particle in an external electromagnetic field. For this model, we prove the existence of generalized gauge transformations. Classical dynamics in Hamiltonian and Lagrangian form is discussed; in particular, the motion in the constant magnetic field is studied in detail.
Two-bath model for activated surface diffusion of interacting adsorbates
Authors: Martínez-Casado R. , Sanz A. S. , Rojas-Lorenzo G. , Miret-Artés S.
Published: February 2010

The diffusion and low vibrational motions of adsorbates on surfaces can be well described by a purely stochastic model, the so-called interacting single adsorbate model, for low-moderate coverages (θ≲0.12). Within this model, the effects of thermal surface phonons and adsorbate-adsorbate collisions are accounted for by two uncorrelated noise functions, which arise in a natural way from a two-bath model based on a generalization of the one-bath Caldeira–Leggett Hamiltonian. As an illustration, the model is applied to the diffusion of Na atoms on a Cu(001) surface with different coverages.
Internal electron transport barrier due to neoclassical ambipolarity in the Helically Symmetric Experiment
Authors: Lore J. , Guttenfelder W. , Briesemeister A. , Anderson D. T. , Anderson F. S. B. , Deng C. B. , Likin K. M. , Spong D. A. , Talmadge J. N. , Zhai K.
Published: February 2010

Electron cyclotron heated plasmas in the Helically Symmetric Experiment (HSX) feature strongly peaked electron temperature profiles; central temperatures are 2.5 keV with 100 kW injected power. These measurements, coupled with neoclassical predictions of large “electron root” radial electric fields with strong radial shear, are evidence of a neoclassically driven thermal transport barrier. Neoclassical transport quantities are calculated using the PENTA code [D. A. Spong, Phys. Plasmas 12, 056114 (2005)], in which momentum is conserved and parallel flow is included. Unlike a conventional stellarator, which exhibits strong flow damping in all directions on a flux surface, quasisymmetric stellarators are free to rotate in the direction of symmetry, and the effect of momentum conservation in neoclassical calculations may therefore be significant. Momentum conservation is shown to modify the neoclassical ion flux and ambipolar ion root radial electric fields in the quasisymmetric configuration. The effect is much smaller in a HSX configuration where the symmetry is spoiled. In addition to neoclassical transport, a model of trapped electron mode turbulence is used to calculate the turbulent-driven electron thermal diffusivity. Turbulent transport quenching due to the neoclassically predicted radial electric field profile is needed in predictive transport simulations to reproduce the peaking of the measured electron temperature profile [Guttenfelder et al., Phys. Rev. Lett. 101, 215002 (2008)].
Performance and emission studies on biodiesel-liquefied petroleum gas dual fuel engine with exhaust gas recirculation
Authors: Ramadhas A. S. , Jayaraj S. , Muraleedharan C.
Published: February 2010

Biodiesel is an alternative fuel to diesel derived from vegetable oils by transesterification process. It can be used in diesel engines with/without any modification in the engine system. Biodiesel engines emit slightly higher NOx emissions, as compared to that of diesel engines, as higher cylinder temperatures achieved during combustion. To reduce the NOx emissions a small percentage of exhaust gases recirculated into the cylinder in dual mode operation. For the improvement of power, liquefied petroleum gas (LPG) was supplied along with fresh air in dual mode operation. This article describes experimental investigation on performance and emission characteristics of single cylinder, indirect diesel engine fueled with biodiesel-diesel blend and LPG in dual fuel mode operation with exhaust gas recirculation (EGR). Recirculation of exhaust gases into the engine decreases the combustion chamber temperatures and marginal improvement in thermal efficiency was observed with EGR. However, reduction in air flow into the engine slightly increases carbon monoxide and hydrocarbon emissions. The exhaust gas temperature of dual fuel engine with EGR is lower than that of engine without EGR.
Quantitative phase imaging with broadband fields
Authors: Wang Zhuo , Popescu Gabriel
Published: February 2010

Recently, Wolf has shown that the phase measurement associated with fields that are not monochromatic, which is relevant for all x-ray structure investigations, must be properly defined via a cross-spectral density function under full spatial coherence conditions; otherwise, the problem is meaningless and has no solution [E. Wolf, Phys. Rev. Lett. 103, 075501 (2009)]. We propose an experimental realization for retrieving the phase across the entire field of an image. The demonstration is performed using broadband optical fields, but can be extended to other electromagnetic radiation, including x-rays.
Accelerating self-consistent field convergence with the augmented Roothaan–Hall energy function
Authors: Hu Xiangqian , Yang Weitao
Published: February 2010

Based on Pulay’s direct inversion iterative subspace (DIIS) approach, we present a method to accelerate self-consistent field (SCF) convergence. In this method, the quadratic augmented Roothaan–Hall (ARH) energy function, proposed recently by Høst and co-workers [J. Chem. Phys. 129, 124106 (2008)], is used as the object of minimization for obtaining the linear coefficients of Fock matrices within DIIS. This differs from the traditional DIIS of Pulay, which uses an object function derived from the commutator of the density and Fock matrices. Our results show that the present algorithm, abbreviated ADIIS, is more robust and efficient than the energy-DIIS (EDIIS) approach. In particular, several examples demonstrate that the combination of ADIIS and DIIS (“ADIIS+DIIS”) is highly reliable and efficient in accelerating SCF convergence.
The “weighted ensemble” path sampling method is statistically exact for a broad class of stochastic processes and binning procedures
Authors: Zhang Bin W. , Jasnow David , Zuckerman Daniel M.
Published: February 2010

The “weighted ensemble” method, introduced by Huber and Kim [Biophys. J. 70, 97 (1996)], is one of a handful of rigorous approaches to path sampling of rare events. Expanding earlier discussions, we show that the technique is statistically exact for a wide class of Markovian and non-Markovian dynamics. The derivation is based on standard path-integral (path probability) ideas, but recasts the weighted-ensemble approach as simple “resampling” in path space. Similar reasoning indicates that arbitrary nonstatic binning procedures, which merely guide the resampling process, are also valid. Numerical examples confirm the claims, including the use of bins which can adaptively find the target state in a simple model.
Multiple diagnostics in a high-pressure hydrogen microwave plasma torch
Authors: Torres J. , van der Mullen J. J. A. M. , Gamero A. , Sola A.
Published: February 2010

We present an experimental study of a hydrogen plasma produced by a microwave axial injection torch, launching the plasma in a helium-filled chamber. Three different diagnostic methods have been used to obtain the electron density and temperature as follows: The Stark intersection method of Balmer spectral lines (already tested in argon and helium plasmas); the modified Boltzmann-plot showing that the plasma is far from the local thermodynamic equilibrium but ruled by the excitation-saturation balance; and a study by the disturbed bilateral relations theory. All of these diagnostic techniques show a good agreement.
The single donator-single acceptor hydrogen bonding structure in water probed by Raman spectroscopy
Authors: Sun Qiang
Published: February 2010

In this work, the Raman spectra of aqueous C12E5 solutions are recorded and utilized to demonstrate the existence of single donator-single acceptor (DA) hydrogen bonding in water. From Raman OH stretching bands of aqueous C12E5 solutions, the relative intensity of 3430 cm−1 subband increases with C12E5 concentrations. For confined water, the DA hydrogen bonding can be expected to be the important hydrogen bonding species. Therefore, the 3430 cm−1 component can be ascribed to OH vibration engaged in DA hydrogen bonding. This is in agreement with our recent explanation on Raman OH stretching band of water. For water at ambient conditions, the double donor-double acceptor (DDAA) and DA should be the dominant hydrogen bonding species, the ratio of DDAA to DA can be approximately to be 0.75:1, and the mean hydrogen bonding can be determined to be 2.75.
A mean field approach for computing solid-liquid surface tension for nanoscale interfaces
Authors: Chiu Chi-cheng , Ranatunga R. J. K. Udayana , Flores David Torres , Pérez D. Vladimir , Moore Preston B. , Shinoda Wataru , Nielsen Steven O.
Published: February 2010

The physical properties of a liquid in contact with a solid are largely determined by the solid-liquid surface tension. This is especially true for nanoscale systems with high surface area to volume ratios. While experimental techniques can only measure surface tension indirectly for nanoscale systems, computer simulations offer the possibility of a direct evaluation of solid-liquid surface tension although reliable methods are still under development. Here we show that using a mean field approach yields great physical insight into the calculation of surface tension and into the precise relationship between surface tension and excess solvation free energy per unit surface area for nanoscale interfaces. Previous simulation studies of nanoscale interfaces measure either excess solvation free energy or surface tension, but these two quantities are only equal for macroscopic interfaces. We model the solid as a continuum of uniform density in analogy to Hamaker’s treatment of colloidal particles. As a result, the Hamiltonian of the system is imbued with parametric dependence on the size of the solid object through the integration limits for the solid-liquid interaction energy. Since the solid-liquid surface area is a function of the size of the solid, and the surface tension is the derivative of the system free energy with respect to this surface area, we obtain a simple expression for the surface tension of an interface of arbitrary shape. We illustrate our method by modeling a thin nanoribbon and a solid spherical nanoparticle. Although the calculation of solid-liquid surface tension is a demanding task, the method presented herein offers new insight into the problem, and may prove useful in opening new avenues of investigation.
High density conics in a magnetically expanding helicon plasma
Authors: Charles C.
Published: February 2010

A two-dimensional mapping of ion density and plasma potential in a diverging magnetized low pressure (0.4 mTorr) carbon dioxide helicon plasma containing a double layer reveals the presence of high density conics (∼7×109 cm−3) along the most diverging magnetic field lines exiting the helicon source and connecting with the grounded expansion chamber. The density in the conic is about 30% greater than the density at the double layer and this results from local ionization associated with the presence of a high energy tail in the electron energy probability function. The plasma potential along the conic is constant at about 30 V.
Partial rootzone drying and deficit irrigation increase stomatal sensitivity to vapour pressure deficit in anisohydric grapevines
Authors: Collins Marisa J. , Fuentes Sigfredo , Barlow Edward W. R.
Published: February 2010

The aim of this study was to investigate how alternative irrigation strategies affected grapevine (Vitis vinifera L.) stomatal response to atmospheric vapour pressure deficit (VPD). In two sites, application of partial rootzone drying (PRD) at 90–100% of crop evapotranspiration (ETc) increased stomatal sensitivity of Shiraz (Syrah) grapevines to high VPD compared with control vines irrigated with the same amount of water but applied on both sides of the vine. PRD significantly reduced vine water use (ESF) measured as sap flow and in dry conditions increased the depth of water uptake from the soil profile. In both experiments, PRD reduced vine water use by up to 50% at moderate VPD (~3 kPa) compared with control vines irrigated at the same level. In the same vines, the response to PRD applied at 100% ETc and deficit irrigation applied at 65% ETc was the same, increasing stomatal sensitivity to VPD and decreasing sap flow. Hydraulic signalling apparently did not play a role in changing stomatal sensitivity as there was no difference in stem water potentials between any of the treatment (PRD and DI) and control vines. This suggests that a long distance root-based chemical signal such as ABA may be responsible for the changes in stomatal behaviour. Shiraz grapevines have previously been classified as anisohydric-like, but application of PRD and DI increased stomatal closure in response to conditions of high evaporative demand making the vines behave in a more isohydric-like manner.
Drought-induced changes in development and function of grapevine (Vitis spp.) organs and in their hydraulic and non-hydraulic interactions at the whole-plant level: a physiological and molecular update
Authors: Lovisolo Claudio , Perrone Irene , Carra Andrea , Ferrandino Alessandra , Flexas Jaume , Medrano Hipolito , Schubert Andrea
Published: February 2010

This review deals with grapevine responses to water stress by examining perturbations to physiological and molecular processes at the root, shoot, leaf and berry levels. Long-distance signalling among organs is also considered. Isohydric or anisohydric Vitis genotypes are described in relation to their response to drought, which is linked to stomatal behaviour. Stomatal regulation of grapevine under abscisic acid and hydraulic control (the latter being linked to embolism formation and recovery in water pathways upstream the stomata) is reviewed and linked to impairments of photosynthetic assimilation. We define three stages of photosynthesis regulation in grapevines that are subjected to progressive water stress on the basis of the main causes of assimilation decline. Early and late contributions of aquaporins, which play a fundamental role in water stress control, are discussed. Metabolic mechanisms of dehydration tolerance are rewieved, and variation linked to differences in transcript abundance of genes involved in osmoregulation, photosynthesis, photorespiration, detoxification of free radicals and coping with photoinhibition. Results of these defence strategies accumulated in berries are reviewed, together with perturbations of their molecular pathways. Features observed in different organs show that grapevine fits well as a complex model plant for molecular and physiological studies on plant drought avoidance/tolerance.
Breeding for improved water productivity in temperate cereals: phenotyping, quantitative trait loci, markers and the selection environment
Authors: Richards Richard A. , Rebetzke Greg J. , Watt Michelle , Condon A. G. (Tony) , Spielmeyer Wolfgang , Dolferus Rudy
Published: February 2010

Consistent gains in grain yield in dry environments have been made by empirical breeding although there is disturbing evidence that these gains may have slowed. There are few examples where an understanding of the physiology and the genetics of putative important drought-related traits has led to improved yields. Success will first depend on identifying the most important traits in the target regions. It will then depend on accurate and fast phenotyping, which, in turn, will lead to: (1) trait-based selection being immediately transferable into breeding operations and (2) being able to identify the underlying genes or the important genomic regions (quantitative trait loci), perhaps leading to efficient marker-based selection (MBS). Genetic complexity, extent of genotype × environment (G × E) interaction and sampling cost per line will determine value of phenotyping over MBS methods. Here, we review traits of importance in dry environments and review whether molecular or phenotypic selection methods are likely to be the most effective in crop improvement programs and where the main bottlenecks to selection are. We also consider whether selection for these traits should be made in dry environments or environments where there is no soil water limitation. The development of lines/populations for trait validation studies and for varietal development is also described. We firstly conclude that despite the spectacular improvements in molecular technologies, fast and accurate phenotyping remains the major bottleneck to enhancing yield gains in water-limited environments. Secondly, for most traits of importance in dry environments, selection is generally conducted most effectively in favourable moisture environments.
Comparing selected fire regime condition class (FRCC) and LANDFIRE vegetation model results with tree-ring data
Authors: Swetnam Tyson L. , Brown Peter M.
Published: February 2010

Fire Regime Condition Class (FRCC) has been developed as a nationally consistent interagency method in the US to assess degree of departure between historical and current fire regimes and vegetation structural conditions across differing vegetation types. Historical and existing vegetation map data also are being developed for the nationwide LANDFIRE project to aid in FRCC assessments. Here, we compare selected FRCC and LANDFIRE vegetation characteristics derived from simulation modeling with similar characteristics reconstructed from tree-ring data collected from 11 forested sites in Utah. Reconstructed reference conditions based on trees present in 1880 compared with reference conditions modeled by the Vegetation Dynamics Development Tool for individual Biophysical Settings (BpS) used in FRCC and LANDFIRE assessments showed significance relationships for ponderosa pine, aspen, and mixed-conifer BpS but not for spruce–fir, piñon–juniper, or lodgepole pine BpS. LANDFIRE map data were found to be ~58% accurate for BpS and ~60% accurate for existing vegetation types. Results suggest that limited sampling of age-to-size relationships by different species may be needed to help refine reference condition definitions used in FRCC assessments, and that more empirical data are needed to better parameterize FRCC vegetation models in especially low-frequency fire types.
The development of fire-induced damage functions for forest recreation activity in Alberta, Canada
Authors: Rausch Michael , Boxall Peter C. , Verbyla Arunas P.
Published: February 2010

This study develops an intertemporal fire damage function for forest recreation activity in the eastern slopes region of the Canadian Rocky Mountains. The methodology employed combined revealed-stated preference data in which the behavioral response variable was annual camping trip frequencies. Photographs were used to portray changes in stand ages and related changes in trip frequencies. The data were analysed using negative binomial count data models. Unlike previous studies employing similar methods, a random effects specification was used to develop trip demand parameters. The results suggest that fires initially decrease annual trips from ~2.56 to 1.0 after the burn. As the stand ages, the effect of the fire decreases until ~12 years after the fire when the trip frequencies recover to about their previous ‘old-growth’ levels. This function is different from others described in the literature for similar mountain ecosystems in North America.
Engineered vascularized bone grafts
Authors: Tsigkou Olga , Pomerantseva Irina , Spencer Joel A. , Redondo Patricia A. , Hart Alison R. , O’Doherty Elisabeth , Lin Yunfeng , Friedrich Claudia C. , Daheron Laurence , Lin Charles P. , Sundback Cathryn A. , Vacanti Joseph P. , Neville Craig
Published: February 2010

Clinical protocols utilize bone marrow to seed synthetic and decellularized allogeneic bone grafts for enhancement of scaffold remodeling and fusion. Marrow-derived cytokines induce host neovascularization at the graft surface, but hypoxic conditions cause cell death at the core. Addition of cellular components that generate an extensive primitive plexus-like vascular network that would perfuse the entire scaffold upon anastomosis could potentially yield significantly higher-quality grafts. We used a mouse model to develop a two-stage protocol for generating vascularized bone grafts using mesenchymal stem cells (hMSCs) from human bone marrow and umbilical cord-derived endothelial cells. The endothelial cells formed tube-like structures and subsequently networks throughout the bone scaffold 4–7 days after implantation. hMSCs were essential for stable vasculature both in vitro and in vivo; however, contrary to expectations, vasculature derived from hMSCs briefly cultured in medium designed to maintain a proliferative, nondifferentiated state was more extensive and stable than that with hMSCs with a TGF-β-induced smooth muscle cell phenotype. Anastomosis occurred by day 11, with most hMSCs associating closely with the network. Although initially immature and highly permeable, at 4 weeks the network was mature. Initiation of scaffold mineralization had also occurred by this period. Some human-derived vessels were still present at 5 months, but the majority of the graft vasculature had been functionally remodeled with host cells. In conclusion, clinically relevant progenitor sources for pericytes and endothelial cells can serve to generate highly functional microvascular networks for tissue engineered bone grafts.
Development and application of in vivo molecular traps reveals that dynein light chain occupancy differentially affects dynein-mediated processes
Authors: Varma Dileep , Dawn Amrita , Ghosh-Roy Anindya , Weil Sarah J. , Ori-McKenney Kassandra M. , Zhao Yanqiu , Keen James , Vallee Richard B. , Williams John C.
Published: February 2010

The ability to rapidly and specifically regulate protein activity combined with in vivo functional assays and/or imaging can provide unique insight into underlying molecular processes. Here we describe the application of chemically induced dimerization of FKBP to create nearly instantaneous high-affinity bivalent ligands capable of sequestering cellular targets from their endogenous partners. We demonstrate the specificity and efficacy of these inducible, dimeric “traps” for the dynein light chains LC8 (Dynll1) and TcTex1 (Dynlt1). Both light chains can simultaneously bind at adjacent sites of dynein intermediate chain at the base of the dynein motor complex, yet their specific function with respect to the dynein motor or other interacting proteins has been difficult to dissect. Using these traps in cultured mammalian cells, we observed that induction of dimerization of either the LC8 or TcTex1 trap rapidly disrupted early endosomal and lysosomal organization. Dimerization of either trap also disrupted Golgi organization, but at a substantially slower rate. Using either trap, the time course for disruption of each organelle was similar, suggesting a common regulatory mechanism. However, despite the essential role of dynein in cell division, neither trap had a discernable effect on mitotic progression. Taken together, these studies suggest that LC occupancy of the dynein motor complex directly affects some, but not all, dynein-mediated processes. Although the described traps offer a method for rapid inhibition of dynein function, the design principle can be extended to other molecular complexes for in vivo studies.
Rapid spread of invasive genes into a threatened native species
Authors: Fitzpatrick Benjamin M. , Johnson Jarrett R. , Kump D. Kevin , Smith Jeramiah J. , Voss S. Randal , Shaffer H. Bradley
Published: February 2010

When introduced or cultivated plants or animals hybridize with their native relatives, the spread of invasive genes into native populations might have biological, aesthetic, and legal implications. Models suggest that the rate of displacement of native by invasive alleles can be rapid and inevitable if they are favored by natural selection. We document the spread of a few introduced genes 90 km into a threatened native species (the California Tiger Salamander) in 60 years. Meanwhile, a majority of genetic markers (65 of 68) show little evidence of spread beyond the region where introductions occurred. Using computer simulations, we found that such a pattern is unlikely to emerge by chance among selectively neutral markers. Therefore, our results imply that natural selection has favored both the movement and fixation of these exceptional invasive alleles. The legal status of introgressed populations (native populations that are slightly genetically modified) is unresolved by the US Endangered Species Act. Our results illustrate that genetic and ecological factors need to be carefully weighed when considering different criteria for protection, because different rules could result in dramatically different geographic areas and numbers of individuals being protected.
Cell type specificity of chromatin organization mediated by CTCF and cohesin
Authors: Hou Chunhui , Dale Ryan , Dean Ann
Published: February 2010

CTCF sites are abundant in the genomes of diverse species but their function is enigmatic. We used chromosome conformation capture to determine long-range interactions among CTCF/cohesin sites over 2 Mb on human chromosome 11 encompassing the β-globin locus and flanking olfactory receptor genes. Although CTCF occupies these sites in both erythroid K562 cells and fibroblast 293T cells, the long-range interaction frequencies among the sites are highly cell type specific, revealing a more densely clustered organization in the absence of globin gene activity. Both CTCF and cohesins are required for the cell-type-specific chromatin conformation. Furthermore, loss of the organizational loops in K562 cells through reduction of CTCF with shRNA results in acquisition of repressive histone marks in the globin locus and reduces globin gene expression whereas silent flanking olfactory receptor genes are unaffected. These results support a genome-wide role for CTCF/cohesin sites through loop formation that both influences transcription and contributes to cell-type-specific chromatin organization and function.
Binding and uptake of H-ferritin are mediated by human transferrin receptor-1
Authors: Li Li , Fang Celia J. , Ryan James C. , Niemi Eréne C. , Lebrón José A. , Björkman Pamela J. , Arase Hisashi , Torti Frank M. , Torti Suzy V. , Nakamura Mary C. , Seaman William E.
Published: February 2010

Ferritin is a spherical molecule composed of 24 subunits of two types, ferritin H chain (FHC) and ferritin L chain (FLC). Ferritin stores iron within cells, but it also circulates and binds specifically and saturably to a variety of cell types. For most cell types, this binding can be mediated by ferritin composed only of FHC (HFt) but not by ferritin composed only of FLC (LFt), indicating that binding of ferritin to cells is mediated by FHC but not FLC. By using expression cloning, we identified human transferrin receptor-1 (TfR1) as an important receptor for HFt with little or no binding to LFt. In vitro, HFt can be precipitated by soluble TfR1, showing that this interaction is not dependent on other proteins. Binding of HFt to TfR1 is partially inhibited by diferric transferrin, but it is hindered little, if at all, by HFE. After binding of HFt to TfR1 on the cell surface, HFt enters both endosomes and lysosomes. TfR1 accounts for most, if not all, of the binding of HFt to mitogen-activated T and B cells, circulating reticulocytes, and all cell lines that we have studied. The demonstration that TfR1 can bind HFt as well as Tf raises the possibility that this dual receptor function may coordinate the processing and use of iron by these iron-binding molecules.
A membrane-associated thioredoxin required for plant growth moves from cell to cell, suggestive of a role in intercellular communication
Authors: Meng Ling , Wong Joshua H. , Feldman Lewis J. , Lemaux Peggy G. , Buchanan Bob B.
Published: February 2010

Thioredoxins (Trxs) are small ubiquitous regulatory disulfide proteins. Plants have an unusually complex complement of Trxs composed of six well-defined types (Trxs
f
,
m
,
x
,
y
,
h
, and
o
) that reside in different cell compartments and function in an array of processes. The extraplastidic
h
type consists of multiple members that in general have resisted isolation of a specific phenotype. In analyzing mutant lines in
Arabidopsis thaliana
, we identified a phenotype of dwarf plants with short roots and small yellowish leaves for AtTrx
h
9 (henceforth, Trx
h
9), a member of the
Arabidopsis
Trx
h
family. Trx
h
9 was found to be associated with the plasma membrane and to move from cell to cell. Controls conducted in conjunction with the localization of Trx
h
9 uncovered another
h
-type Trx in mitochondria (Trx
h
2) and a Trx in plastids earlier described as a cytosolic form in tomato. Analysis of Trx
h
9 revealed a 17-amino acid N-terminal extension in which the second Gly (Gly
2
) and fourth cysteine (Cys
4
) were highly conserved. Mutagenesis experiments demonstrated that Gly
2
was required for membrane binding, possibly via myristoylation. Both Gly
2
and Cys
4
were needed for movement, the latter seemingly for protein structure and palmitoylation. A three-dimensional model was consistent with these predictions as well as with earlier evidence showing that a poplar ortholog is reduced by a glutaredoxin rather than NADP-thioredoxin reductase. In demonstrating the membrane location and intercellular mobility of Trx
h
9, the present results extend the known boundaries of Trx and suggest a role in cell-to-cell communication.
Two closely related endocytic proteins that share a common OCRL-binding motif with APPL1
Authors: Swan Laura E. , Tomasini Livia , Pirruccello Michelle , Lunardi Joël , De Camilli Pietro
Published: February 2010

Mutations of the inositol 5′ phosphatase oculocerebrorenal syndrome of Lowe (OCRL) give rise to the congenital X-linked disorders oculocerebrorenal syndrome of Lowe and Dent disease, two conditions giving rise to abnormal kidney proximal tubule reabsorption, and additional nervous system and ocular defects in the case of Lowe syndrome. Here, we identify two closely related endocytic proteins, Ses1 and Ses2, which interact with the ASH-RhoGAP–like (ASPM-SPD-2-Hydin homology and Rho-GTPase Activating Domain-like) domain of OCRL. The interaction is mediated by a short amino acid motif similar to that used by the rab-5 effector APPL1 (Adaptor Protein containing pleckstrin homology [PH] domain, PTB domain and Leucine zipper motif 1) APPL1 for OCRL binding. Ses binding is mutually exclusive with APPL1 binding, and is disrupted by the same missense mutations in the ASH-RhoGAP–like domain that also disrupt APPL1 binding. Like APPL1, Ses1 and -2 are localized on endosomes but reside on different endosomal subpopulations. These findings define a consensus motif (which we have called a phenylalanine and histidine [F&H] motif) for OCRL binding and are consistent with a scenario in which Lowe syndrome and Dent disease result from perturbations at multiple sites within the endocytic pathway.
NIP45 controls the magnitude of the type 2 T helper cell response
Authors: Fathman John W. , Gurish Michael F. , Hemmers Saskia , Bonham Kevin , Friend Daniel S. , Grusby Michael J. , Glimcher Laurie H. , Mowen Kerri A.
Published: February 2010

Nuclear factor of activated T cell (NFAT) transcription factors are key regulators of gene transcription within immune cells. The NFAT-interacting protein, (NIP45), augments NFAT-driven IL-4 expression by a mechanism that relies on arginine methylation. To establish the function of NIP45 in vivo, we generated mice with a targeted deletion of the gene encoding this cofactor.NIP45-deficient T helper cells displayed profound defects in the expression of NFAT-regulated cytokine genes, including IL-4. WhereasNIP45deficiency does not interfere with T helper cell NFAT activation or lineage-specific transcription-factor expression, NIP45 acts as an enhancer for the assembly of protein arginine methyltransferase 1 and the protein arginine methyltransferase 1-linked histone 4 arginine 3 methylation with the IL-4 promoter. Our study reveals an essential role for NIP45 in promoting robust cytokine expression in vivo, which is required for the efficient handling of parasites. We propose that NIP45 acts as a molecular rheostat serving to amplify the type-2 immune response.
Cancer stem cells from colorectal cancer-derived cell lines
Authors: Yeung Trevor M. , Gandhi Shaan C. , Wilding Jennifer L. , Muschel Ruth , Bodmer Walter F.
Published: February 2010

Cancer stem cells (CSCs) are the subpopulation of cells within a tumor that can self-renew, differentiate into multiple lineages, and drive tumor growth. Here we describe a two-pronged approach for the identification and characterization of CSCs from colorectal cancer cell lines, using a Matrigel-based differentiation assay, and cell surface markers CD44 and CD24. About 20 to 30% of cells from the SW1222 cell line form megacolonies in Matrigel that have complex 3D structures resembling colonic crypts. The megacolonies’ capacity to self-renew in vitro is direct evidence that they contain the CSCs. Furthermore, just 200 cells from SW1222 megacolonies initiate tumors in NOD/SCID mice. We also showed that CD44
+
CD24
+
cells enriched for colorectal CSCs in the HT29 and SW1222 cell lines, which can self-renew and reform all four CD44/CD24 subpopulations, are the most clonogenic in vitro and can initiate tumors in vivo. A single SW1222 CD44
+
CD24
+
CSC, when grown in Matrigel, can form large megacolonies that differentiate into enterocyte, enteroendocrine, and goblet cell lineages. The HCT116 line does not differentiate or express CDX1, nor does it contain subpopulations of cells with greater tumor-forming capacity, suggesting that HCT116 contains mainly CSCs. However, forced expression of CDX1 in HCT116 leads to reduced clonogenicity and production of differentiating crypt-containing colonies, which can explain the selection for reduced CDX1 expression in many colorectal cancers. In summary, colorectal cancer cell lines contain subpopulations of CSCs, characterized by their cell surface markers and colony morphology, which can self-renew and differentiate into multiple lineages.
Cortisol and symptoms of psychopathology in Russian and American college students
Authors: Tennison Linda R. , Rodgers Laura S. , Beker David , Vorobjeva Klarisa I. , Creed Evan T. , Simonenko Alena
Published: February 2010

Cortisol is a key player in the hypothalamus–pituitary–adrenal (HPA) axis response to stress, and has been related to symptoms of depression and other stress‐related pathology. The present study investigated the relationship between cortisol and survey measures of stress and psychopathology as well as lifestyle in Russian and American college students. Salivary cortisol was collected upon awakening, 30 min later, at 4 p.m., and at 10 p.m. by Russian and American college students. Survey measures of anxiety and depression, as measured by the Hopkins Symptom Checklist (HSCL‐25) were collected as well as scores on the Trauma History Questionnaire (THQ). In addition, measures of drinking‐related problems, as measured by the Alcohol Use Disorder Identification Test (AUDIT) and the “Cut down, Annoyed, Guilty, Eye‐opener” (CAGE) were also completed. Consistent with the typically observed empirical pattern, cortisol levels increased in the 30 min after awakening and then declined across the day. Women reported more symptoms of anxiety than did men in both Russian and American samples. American students reported more symptoms of depression than did Russian students, though Russian students reported more traumatic life experiences. Americans had higher cortisol levels overall, though Russian students had larger changes in cortisol levels across the day, associated with both greater morning rises and afternoon declines in cortisol. While more Russian students reported smoking, American students reported more problems associated with alcohol use as measured by the AUDIT. The relationship between stress and health, mediating factors of lifestyle and coping, and the impact of social transition in Russia are discussed.
GENDER INEQUALITIES AND THE ROLE OF MONEY IN SPANISH DUAL-INCOME COUPLES
Authors: Dema-Moreno Sandra , Díaz-Martínez Capitolina
Published: February 2010

This article analyses to what extent the incorporation of women into the labour market and their consequent economic contribution to family income affects couple's relationships. We focus particularly on Spanish couples, using a qualitative method that consists of 48 in-depth interviews of 16 couples. The partners in each couple were first interviewed together and then separately. From the analysis of the interviews, we have identified three types of dual-income couples: ‘traditional’, ‘egalitarian’ and ‘false egalitarian’ couples. According to our findings, these three types of couples differ in the meaning that men and women attribute to money and in the dynamics and processes related to the control and expenditure of money. Whereas for the majority of women money is linked to personal autonomy, their salaries do not automatically generate a balance between the partners. Moreover, despite social changes, gender socialisation and gender roles persist within the couple, reinforcing, for instance, the belief that men symbolically remain the main providers in dual-income couples.
Synchrotron x-ray diffraction measurements of strain in metallic nanoparticles with oxide shells
Authors: Ingham B , Hendy S C , Fong D D , Fuoss P H , Eastman J A , Lassesson A , Tee K C , Convers P Y , Brown S A , Ryan M P , Toney M F
Published: February 2010

We describe synchrotron x-ray diffraction measurements of strain in Cu and Pd metal nanoparticles (1.7–40 nm diameter) both with an air-formed oxide shell and after reduction of the oxide by treatment in a hydrogen-containing atmosphere. Oxide removal is evident from x-ray diffraction (for Cu) and x-ray absorption spectroscopy (for Pd). A simple model that uses bulk elastic properties is applied to each system. In the Pd case the model predictions agree well with the experiment. For Cu the observed strains are much smaller than predicted. This discrepancy is attributed to (a) the presence of multiple grains within the Cu particles and (b) the incoherency of the oxide with the metal core.
Diabolic points and entanglement
Authors: Steeb Willi-Hans
Published: February 2010

Diabolic points and entanglement for a hierarchy of spin Hamilton operators acting in the finite-dimensional Hilbert space are investigated.