bluuebunny/crossref_metadata_2025 huggingface dataset:
Species-related luminescence-structure relationships in europium-exchanged mesoporous material
Authors: Tiseanu C. , Kumke M. U. , Parvulescu V. I. , Martens J.
Published: March 2009

Europium exchanged into a mesoporous material (Zeotile-1) was extensively characterized with respect to the Si/Al ratio and surface silylation by using time-resolved emission spectroscopy. Qualitative as well as quantitative details of the europium species-related luminescence-structure relationships were obtained and discussed such as the decay associated spectra, local distortion and structure of the bonding environment, crystal-field strength, radiative relaxation rates, and the quantum efficiency. Thus, two europium species were found in the parent as well as in the silylated materials: one species located on the internal surface and the second inside the 2–2.5 nm pores. The species located on the internal surface is characterized by photoluminescence decay times of 105 μs<τ<125 μs, an asymmetry value R of 0.6<R<0.8, and a quantum efficiency of 2%–2.5%. Upon silylation, the photoluminescence decay times, the asymmetry values, and the quantum efficiency were increased to 160 μs<τ<180 μs, 1.7<R<2.1, and ∼4%, respectively. Following silylation, the number of water molecules is reduced in the first coordination shell of the europium species located on the internal surface from eight to nine to about five. On the other hand, the europium species located inside the pores showed a much longer photoluminescence decay time (460 μs<τ<560 μs) and a much higher asymmetry ratio (5<R<6.5). The related photoluminescence efficiency was 26%–30%. An average of one up to two water molecules in the first coordination shell of the europium species located inside the pores was estimated for both parent and silylated materials.
Shock propagation in a cemented tungsten carbide
Authors: Appleby-Thomas G. J. , Hazell P. J. , Stennett C. , Cooper G. , Helaar K. , Diederen A. M.
Published: March 2009

WC-based ceramic metal composites (cermets) are of great importance in both armor and munition design due to the combination of properties imparted by the presence of two different phases. WC–Co cermets are of interest in this area due to the hardness and strength imparted by the WC phase while the cementing Co matrix acts to increase plasticity and toughness. Here the dynamic response of G13 WC–Co manufactured by Kennametal Engineered Products B.V. was studied via a series of plate impact experiments involving both longitudinal and lateral gauges, which allowed determination of the Us−Up relationship, measurement of a Hugoniot elastic limit of 3.3±0.2 GPa, measurement of a spall strength of 4.38 GPa, and an investigation of the stress dependence of shear strength in such a strong material.
Evidence of a thermally stimulated charge transfer mechanism and interface defect formation in metal-oxide-semiconductor structures with germanium nanocrystals
Authors: Beyer Reinhard , von Borany Johannes
Published: March 2009

The trapping of charge carriers and the mechanism of the charge transfer were examined in metal-oxide-semiconductor structures with germanium nanocrystals embedded in a 20nm silicondioxide layer. The nanoclusters were generated by ion beam synthesis. Capacitance-voltage (C-V) measurements exhibit a hysteresis loop due to the charge trapping and detrapping. Effective oxide trap densities were derived and could be related to the nanoclusters. A strong temperature dependence of the C-V loop indicates that a thermally stimulated process is involved in the charge transfer between the clusters and the interface, thus ruling out a direct tunneling. The use of deep level transient spectroscopy revealed a large amount of interface states in the Ge implanted samples, including a distinct trap state at 0.32eV above the valence band edge with a concentration up to 2×1013cm−2eV−1, which is much likely involved in the emission of carriers from cluster-related states in a two-stage process.
Multisymplectic Preissman scheme for the time-domain Maxwell’s equations
Authors: Cai Jiaxiang , Wang Yushun , Qiao Zhonghua
Published: March 2009

From the Bridges’ multisymplectic form of Maxwell’s equations, we derive a multisymplectic Preissman scheme which couples two time levels for 2+1 dimensional Maxwell’s equations. The scheme is proven to preserve the discrete local energy exactly. Numerical results are reported to illustrate that the scheme is effective and it can get more precise numerical solutions than Yee’s scheme. Our numerical results can also indicate that the scheme keeps the discrete local energy and the global energy very well.
Nonlinear Rayleigh–Taylor instabilities in fast Z pinches
Authors: Miles Aaron R.
Published: March 2009

A simplified analytic model is presented to describe the implosion of a plasma column by an azimuthal magnetic field of sufficient magnitude to drive a strong shock wave into the plasma. This model is employed together with buoyancy-drag-based models of nonlinear single-mode and turbulent multimode Rayleigh–Taylor growth to investigate the mixing process in such fast Z pinches. These models give predictions that characterize limitations the instability can impose on the implosion in terms of maximum convergence ratios attainable for an axially coherent pinch. Both the implosion and instability models are validated with results from high-resolution numerical simulations.
Highly accurate tau-leaping methods with random corrections
Authors: Hu Yucheng , Li Tiejun
Published: March 2009

We aim to construct higher order tau-leaping methods for numerically simulating stochastic chemical kinetic systems in this paper. By adding a random correction to the primitive tau-leaping scheme in each time step, we greatly improve the accuracy of the tau-leaping approximations. This gain in accuracy actually comes from the reduction in the local truncation error of the scheme in the order of τ, the marching time step size. While the local truncation error of the primitive tau-leaping method is O(τ2) for all moments, our Poisson random correction tau-leaping method, in which the correction term is a Poisson random variable, can reduce the local truncation error for the mean to O(τ3), and both Gaussian random correction tau-leaping methods, in which the correction term is a Gaussian random variable, can reduce the local truncation error for both the mean and covariance to O(τ3). Numerical results demonstrate that these novel methods more accurately capture crucial properties such as the mean and variance than existing methods for simulating chemical reaction systems. This work constitutes a first step to construct high order numerical methods for simulating jump processes. With further refinement and appropriately modified step-size selection procedures, the random correction methods should provide a viable way of simulating chemical reaction systems accurately and efficiently.
Toward a better physical understanding of a-Si:H/c-Si heterojunction solar cells
Authors: Damon-Lacoste J. , Roca i Cabarrocas P.
Published: March 2009

Despite energy conversion efficiencies exceeding 22%, current understanding of the physics behind heterojunction solar cells remains incomplete. The role of hydrogen and ion bombardment during the plasma deposition as well as the influence of an epitaxial layer remains a subject of debate. Our results suggest that hydrogen plays a key role in the fabrication of high efficiency heterojunction solar cells. We show that ion bombardment is not as detrimental as is often thought. Moreover we find that an epitaxial layer is not necessarily harmful to the cell’s Voc. We propose a criterion linking the layer’s epitaxy and the cells’ performance. To further investigate the role of the H2 plasma, we carry out in situ ellipsometry measurements on various kinds of c-Si wafers. The effects of this H2 plasma strongly depend on the resistivity of the c-Si wafer, suggesting that plasma conditions must be tuned to optimize cell efficiency according to the c-Si resistivity.
Analytical strain relaxation model for Si1−xGex/Si epitaxial layers
Authors: Menéndez José
Published: March 2009

An approximate but accurate analytical solution is presented for the system of differential equations used by Houghton to model kinetically limited strain relaxation in Si1−xGex alloys layers growing on Si substrates [J. Appl. Phys. 70, 2136 (1991)]. This solution makes it much easier to compare the relaxation model with experimental data. The analytical results are used to refit the Houghton model parameter n0 (representing the initial heterogeneous density of dislocation sources) to published relaxation data, including post-1991 experimental work. The fits, which include experiments in which the growth temperature ranged from 450 to 750 °C, show considerable scattering in n0, but suggests that n0 increases as the growth temperature is lowered. Since this trend was not apparent in the original Houghton work, a detailed analysis is carried out for samples grown and annealed at temperatures below 450 °C. For this purpose, the Houghton model is extended to include the reduction in effective stress as the strain relaxation advances as well as the effect of dislocation pinning. The analysis confirms that n0 increases as the growth temperature is lowered. Possible physical reasons are discussed, and an empirical fit to the temperature dependence of n0 is used to generate revised predictions of apparent critical thicknesses.
Electric amplification of the magnetoplastic effect in nonmagnetic crystals
Authors: Alshits V. I. , Darinskaya E. V. , Koldaeva M. V. , Petrzhik E. A.
Published: March 2009

An experimental study of the electric field influence on the magnetoplasticity is performed for NaCl and LiF crystals. It is shown that even rather weak electric fields of E∼1–10 kV/m strongly amplify the magnetoplastic effects of both “signs.” In crystals, such as NaCl(Ca), where the magnetic transformation of impurities in dislocation cores decreases the dislocation pinning, the mean dislocation path l in the magnetic field B abruptly increases under an electric field applied along with B. Also in crystals such as NaCl(Pb), where, conversely, a magnetically induced growth of the pinning force occurs, the electric field again amplifies the magnetic effect, this time suppressing a dislocation mobility. In both cases, no electric effects at B=0 are observed. Measurements at the temperatures of 77, 165, and 293 K displayed a thermally activated character of the electric actions. An activation analysis was performed for the two types of NaCl crystals, manifesting a magnetic softening. The found activation energies, U(E), revealed a monotonous decrease in E and coinciding magnitudes U(0)≈0.2 eV. It was also shown that an electric field does not destroy the dependencies of the mean dislocation path l on the induction B and the impurity concentration C:l∝1/C[1+(B0/B)2]. The observed electric effects can be associated with electromigration of charged cation vacancies in the vicinity of dislocation cores. This apparently increases the number of magnetically active pinning ions Me+ of the bivalent impurity Me (say, Ca, Mg, etc.) replacing the ordinary diamagnetic ions Me2+. Analogous effects are also expected in ferroelectrics and semiconductors.
Small tin cluster anions: Transition from quasispherical to prolate structures
Authors: Oger Esther , Kelting Rebecca , Weis Patrick , Lechtken Anne , Schooss Detlef , Crawford Nathan R. M. , Ahlrichs Reinhart , Kappes Manfred M.
Published: March 2009

The structures and energetics of small tin cluster Snn− anions up to n=15 were determined by a combination of density-functional theory and three different experimental methods: Ion mobility spectrometry, trapped ion electron diffraction, and collision induced dissociation. We find compact, quasispherical structures up to n=12. Sn12− is a slightly distorted hollow icosahedron while Sn13− to Sn15− have prolate structures, consisting of merged, hollow, in part incomplete, deltahedral subunits: Sn13− consists of a face-sharing pentagonal bipyramid and tricapped trigonal bipyramid, Sn14− comprises a face-sharing dicapped trigonal prism and capped square-antiprism, and Sn15− consists of two face-sharing tricapped trigonal prisms.
Resonant behavior observed in electron field emission from acid functionalized multiwall carbon nanotubes
Authors: Lyth S. M. , Silva S. R. P.
Published: March 2009

Acid functionalized multiwall carbon nanotube ink was deposited onto carbon fiber fabric via dip coating. Repeatable staircaselike current-field curves were observed in the field emission data. These atypical curves are attributed to resonant tunneling through localized surface states in a quantum well structure, which arises due to the presence of the surface carboxylic functional group.
Phonon effects on zero-phonon transitions between Stark levels in NaBi(WO4)2:Yb3+
Authors: Demirkhanyan Gagik G. , Demirkhanyan Hasmik G. , Kokanyan Edvard P. , Kostanyan Radik B. , Gruber John B. , Nash Kelly L. , Sardar Dhiraj K.
Published: March 2009

We report results from a modeling study of temperature-dependent line broadening and associated Debye–Waller factors (DWFs) for zero-phonon transitions between the F2J (J=7/2,5/2) manifolds of Yb3+ in NaBi(WO4)2. The Hamiltonian includes the electron-phonon interaction between the electronic states of the Yb3+ (4f13) ions and the lattice (Debye) phonon spectrum of the host crystal in a second quantization formulation. The temperature dependences of the linewidths, DWFs, and the intensities of the transitions are reported in terms of the ratio of temperature to Debye temperature (T/TD). Of particular interest is the temperature dependence of the most intense transitions at emission wavelengths of 996.6 and 1010.2 nm. These transitions are the best candidates for low-threshold stimulated emission based on measured emission cross sections and lifetimes. We find that with a decrease in temperature, an abrupt increase in radiation intensity occurs for the 1010.2 nm emission transition, suggesting that an optimum temperature value for a maximum stimulated emission may be obtained for Yb3+ in this disordered structure.
A dedicated superbend x-ray microdiffraction beamline for materials, geo-, and environmental sciences at the advanced light source
Authors: Kunz Martin , Tamura Nobumichi , Chen Kai , MacDowell Alastair A. , Celestre Richard S. , Church Matthew M. , Fakra Sirine , Domning Edward E. , Glossinger James M. , Kirschman Jonathan L. , Morrison Gregory Y. , Plate Dave W. , Smith Brian V. , Warwick Tony , Yashchuk Valeriy V. , Padmore Howard A. , Ustundag Ersan
Published: March 2009

A new facility for microdiffraction strain measurements and microfluorescence mapping has been built on beamline 12.3.2 at the advanced light source of the Lawrence Berkeley National Laboratory. This beamline benefits from the hard x-radiation generated by a 6 T superconducting bending magnet (superbend). This provides a hard x-ray spectrum from 5 to 22 keV and a flux within a 1 μm spot of ∼5×109 photons/s (0.1% bandwidth at 8 keV). The radiation is relayed from the superbend source to a focus in the experimental hutch by a toroidal mirror. The focus spot is tailored by two pairs of adjustable slits, which serve as secondary source point. Inside the lead hutch, a pair of Kirkpatrick–Baez (KB) mirrors placed in a vacuum tank refocuses the secondary slit source onto the sample position. A new KB-bending mechanism with active temperature stabilization allows for more reproducible and stable mirror bending and thus mirror focusing. Focus spots around 1 μm are routinely achieved and allow a variety of experiments, which have in common the need of spatial resolution. The effective spatial resolution (∼0.2 μm) is limited by a convolution of beam size, scan-stage resolution, and stage stability. A four-bounce monochromator consisting of two channel-cut Si(111) crystals placed between the secondary source and KB-mirrors allows for easy changes between white-beam and monochromatic experiments while maintaining a fixed beam position. High resolution stage scans are performed while recording a fluorescence emission signal or an x-ray diffraction signal coming from either a monochromatic or a white focused beam. The former allows for elemental mapping, whereas the latter is used to produce two-dimensional maps of crystal-phases, -orientation, -texture, and -strain/stress. Typically achieved strain resolution is in the order of 5×10−5 strain units. Accurate sample positioning in the x-ray focus spot is achieved with a commercial laser-triangulation unit. A Si-drift detector serves as a high-energy-resolution (∼150 eV full width at half maximum) fluorescence detector. Fluorescence scans can be collected in continuous scan mode with up to 300 pixels/s scan speed. A charge coupled device area detector is utilized as diffraction detector. Diffraction can be performed in reflecting or transmitting geometry. Diffraction data are processed using XMAS, an in-house written software package for Laue and monochromatic microdiffraction analysis.
A new criterion to distinguish stochastic and deterministic time series with the Poincaré section and fractal dimension
Authors: Golestani Abbas , Jahed Motlagh M. R. , Ahmadian K. , Omidvarnia Amir H. , Mozayani Nasser
Published: March 2009

In this paper, we propose a new method for detecting regular behavior of time series: this method is based on the Poincaré section and the Higuchi fractal dimension. The new method aims to distinguish random signals from deterministic signals. In fact, our method provides a pattern for decision making about whether a signal is random or deterministic. We apply this method to different time series, such as chaotic signals, random signals, and periodic signals. We apply this method to examples from all types of route to chaotic signals. This method has also been applied to data about iris tissues. The results show that the new method can distinguish different types of signals.
CO ppb sensors based on monodispersed SnOx:Pd mixed nanoparticle layers: Insight into dual conductance response
Authors: Aruna I. , Kruis F. E. , Kundu S. , Muhler M. , Theissmann R. , Spasova M.
Published: March 2009

This study reports the modifications in CO sensing of SnOx nanoparticle layers by utilizing monodispersed Pd nanoparticles. The distinct advantage of monosized particles and contaminant-free samples with open porosity in addition to size effects resulted in improved CO sensing with decrease in Pd nanoparticle size to 5 nm, decreasing the lowest detection levels of CO using SnOx-based sensor technology down to 10 ppb (parts per billion) in dry synthetic air. The homogeneously mixed nanoparticle layers also exhibit discrimination capability between CO and ethanol in dry air as a manifestation of the dual conductance response. Detailed x-ray photoelectron spectroscopy studies clearly reveal “Mars–van Krevelen” as the key mechanism responsible for the observed sensing in mixed nanoparticle layers. The interfacial/surface PdO formed upon pretreatment in air is continuously “consumed” and “reformed” upon exposure, respectively, to CO and synthetic air. In contrast to the case of ethanol exposure with n-type response, the Pd aided reduction of tin oxide surface in CO ambient leads to p-type response. The sensors of the present study have a wide range of promising applications from air quality control to food and fuel industries.
Influence of stabilizers in ZnO nanodispersions on field-effect transistor device performance
Authors: Bubel Simon , Nikolova Donna , Mechau Norman , Hahn Horst
Published: March 2009

In order to build printable inorganic electronic devices, semiconducting suspensions are needed, which can be processed at low temperatures using low-cost manufacturing techniques. Stabilized suspensions made of zinc oxide (ZnO) nanoparticles were used to fabricate field-effect transistors by spin coating. The performance of the devices is strongly affected by the nature and concentration of the compounds added to stabilize the nanodispersions. An increase in the field-effect mobility by more than one order of magnitude is obtained upon increasing the stabilizer concentration from 3 to 13 wt %. A further increase in the concentration above 13 wt % results in a decrease in the field-effect mobility. This behavior can be explained by changes in the morphology, the particle-particle junction, and the passivation of surface defect sites.
Charge transport in transparent conductors: A comparison
Authors: Sangeeth C. S. Suchand , Jaiswal Manu , Menon Reghu
Published: March 2009

A comparative investigation of charge transport properties is presented, for polymeric [poly(3,4-ethylenedioxythiophene):poly(styrenesulfonate) (PEDOT:PSS)], single-wall carbon nanotube (SWNT) and inorganic (indium tin oxide, ITO), transparent conducting electrodes. The polymeric and nanotube systems show hopping transport at low temperatures, in contrast with the disordered-metal transport in ITO. The low temperature magnetotransport (up to 11 T) and high electric-field transport (up to 500 V/cm) indicate the significant role of nanoscopic scale disorder for charge transport in polymer and nanotube based systems. The results show that characteristic length scales like localization length correlates with the nanomorphology in these systems. Further, the high frequency conductivity measurements (up to 30 MHz) in PEDOT:PSS and SWNT follow the extended pair approximation model [σ(ω)=σ(0)[1+(ω/ω0)s].
Critical assessment of diffusion coefficients in semidilute to concentrated solutions of polystyrene in toluene
Authors: Pollak T. , Köhler W.
Published: March 2009

We have measured collective diffusion coefficients of dilute, semidilute, and concentrated solutions of polystyrene in toluene up to a polymer concentration of 0.832 mass fractions at T=25 °C. The three employed experimental techniques of photon correlation spectroscopy, thermal diffusion forced Rayleigh scattering, and optical beam deflection cover four orders of magnitude with respect to their characteristic diffusion lengths (200 nm–2.9 mm), corresponding to more than 8 decades of the diffusion time constants. Contrary to existing literature data, which suggest a length scale dependent anomalous diffusion at high concentrations, all our techniques yield identical diffusion coefficients and purely Fickian diffusion, irrespective of their characteristic length scale.
A Chebychev propagator for inhomogeneous Schrödinger equations
Authors: Ndong Mamadou , Tal-Ezer Hillel , Kosloff Ronnie , Koch Christiane P.
Published: March 2009

A propagation scheme for time-dependent inhomogeneous Schrödinger equations is presented. Such equations occur in time dependent optimal control theory and in reactive scattering. A formal solution based on a polynomial expansion of the inhomogeneous term is derived. It is subjected to an approximation in terms of Chebychev polynomials. Different variants for the inhomogeneous propagator are demonstrated and applied to two examples from optimal control theory. Convergence behavior and numerical efficiency are analyzed.
Systematic study on work-function-shift in metal/Hf-based high-k gate stacks
Authors: Kita Yuki , Yoshida Shinichi , Hosoi Takuji , Shimura Takayoshi , Shiraishi Kenji , Nara Yasuo , Yamada Keisaku , Watanabe Heiji
Published: March 2009

Change in the work function (WF) of the gate electrode material caused by the contact with Hf-based high-k gate dielectrics was investigated by means of the flat-band voltage (Vfb) shift in capacitance-voltage curves, and the interface dipole, which modifies the WF, was characterized by x-ray photoelectron spectroscopy. We observed a negative Vfb shift and corresponding interface dipole, which suggest the formation of oxygen vacancy (VO) in the Hf-based oxides. In contrast, we observed an opposite (positive) Vfb shift and interface dipole when Au electrodes were formed on cleaned Hf-based dielectrics. This indicates that Au–Hf bond hybridization at the Au/HfSiON interface also causes effective WF modulation, as theoretically predicted by Shiraishi et al. (Tech. - Dig. Int. Electron Devices Meet. 2005, 43).
Ecology of the rare but irruptive Pilliga mouse (Pseudomys pilligaensis). I. Population fluctuation and breeding season
Authors: Tokushima Hideyuki , Green Stuart W. , Jarman Peter J.
Published: March 2009

During a 4-year study in the Pilliga Scrub, trappable densities of the Pilliga mouse, Pseudomys pilligaensis (Muridae), were low before a wildfire in November 1997, higher in late 1999 and February 2000 (5–30 mice ha−1) and very high (up to 83 mice ha−1) in April 2000; however, the densities fell sharply by July 2000, remaining low (0–5 mice ha−1) until trapping ended in October 2001. Site-specific densities and their fluctuations differed among the four trapping sites, although fluctuations were broadly synchronised by the irruption peak. Within-site distribution changed as density fluctuated, from sparse to almost ubiquitous and back to sparse, and within-grid pre-irruption distributions did not predict those after the irruption. After the population decline, mice virtually disappeared from three of the four sites. The species’ breeding season spanned at least October–April; some females bred repeatedly within a season. Prolonged good rains soon after the wildfire may have facilitated the irruption. The study suggested that P. pilligaensis is distributed in disjunct patches of (refuge) habitat within its range except when environmental conditions are favourable, and that it is able to irrupt and become briefly ubiquitous before suddenly declining to a low density and sparse distribution. We suggest approaches for monitoring of this rare species.
Ecology of the rare but irruptive Pilliga mouse (Pseudomys pilligaensis). II. Demography, home range and dispersal
Authors: Tokushima Hideyuki , Jarman Peter J.
Published: March 2009

We report aspects of demography, home range and movement of the rare Pilliga mouse, Pseudomys pilligaensis, during a population irruption, peaking in April 2000, and the subsequent decline. Population median weights were lower before than at, or after, the irruption peak. Individual mice grew more strongly immediately before the peak than later. The initial weight negatively influenced the growth rate, more so at the irruption peak than before it. At peak, mice at previously occupied sites were heavier than those at recently occupied sites, and male-biased, compared with the female-biased mice dispersing into new sites. The population at the most densely occupied site was strongly female-biased just before and at peak; female dispersers tended to survive better than males. After the irruption, residents survived better than the newly established mice at the only site that retained moderate densities. Individual movements mostly did not differ between sexes, or among sites or size classes. Range overlap, more extensive in spring than in other seasons, was equally frequent within and between sexes. The irruption was apparently initiated by spring breeding in a non-territorial population, with rapid individual growth, and led to dispersal especially by a female-biased subpopulation of lighter (and perhaps younger) mice. After the irruption peak, the rapid growth in weight stopped, suggesting resource restriction, and the social system may no longer have been non-territorial.
Mammalian cell penetration, siRNA transfection, and DNA transfection by supercharged proteins
Authors: McNaughton Brian R. , Cronican James J. , Thompson David B. , Liu David R.
Published: March 2009

Nucleic acid reagents, including small interfering RNA (siRNA) and plasmid DNA, are important tools for the study of mammalian cells and are promising starting points for the development of new therapeutic agents. Realizing their full potential, however, requires nucleic acid delivery reagents that are simple to prepare, effective across many mammalian cell lines, and nontoxic. We recently described the extensive surface mutagenesis of proteins in a manner that dramatically increases their net charge. Here, we report that superpositively charged green fluorescent proteins, including a variant with a theoretical net charge of +36 (+36 GFP), can penetrate a variety of mammalian cell lines. Internalization of +36 GFP depends on nonspecific electrostatic interactions with sulfated proteoglycans present on the surface of most mammalian cells. When +36 GFP is mixed with siRNA, protein–siRNA complexes ≈1.7 μm in diameter are formed. Addition of these complexes to five mammalian cell lines, including four that are resistant to cationic lipid-mediated siRNA transfection, results in potent siRNA delivery. In four of these five cell lines, siRNA transfected by +36 GFP suppresses target gene expression. We show that +36 GFP is resistant to proteolysis, is stable in the presence of serum, and extends the serum half-life of siRNA and plasmid DNA with which it is complexed. A variant of +36 GFP can mediate DNA transfection, enabling plasmid-based gene expression. These findings indicate that superpositively charged proteins can overcome some of the key limitations of currently used transfection agents.
Design of a mechanical clutch-based needle-insertion device
Authors: Bassett Erik K. , Slocum Alexander H. , Masiakos Peter T. , Pryor Howard I. , Farokhzad Omid C. , Karp Jeffery M.
Published: March 2009

Insertion of trocars, needles, and catheters into unintended tissues or tissue compartments results in hundreds of thousands of complications annually. Current methods for blood vessel cannulation or epidural, chest tube, and initial trocar placement often involve the blind pass of a needle through several layers of tissue and generally rely on distinguishable anatomic landmarks and a high degree of clinical skill. To address this simply and without the use of electronics, a purely mechanical clutch system was developed for use in medical devices that access tissue and tissue compartments. This clutch utilizes the surface contact of a buckled filament inside an S-shaped tube to transmit force from the filament (catheter/guide wire) to the tube (needle). Upon encountering sufficient resistance at the tip, such as dense tissue, the catheter buckles and locks within the tube, causing the filament and needle to advance as one. When the needle reaches the target tissue or fluid-filled cavity, the filament unlocks and slides freely into the target region while the needle remains stationary. A similar locking phenomenon has long been observed in drill strings inside drill shafts used by the oil-drilling industry, and oil industry models were adapted to describe the motion of this clutch system. A predictive analytical model was generated and validated with empirical data and used to develop prototypes of a complete device then tested in vitro on muscle tissue and in vivo on a porcine laparoscopic model with promising results.
SDF-1α stimulates JNK3 activity via eNOS-dependent nitrosylation of MKP7 to enhance endothelial migration
Authors: Pi Xinchun , Wu Yaxu , Ferguson James E. , Portbury Andrea L. , Patterson Cam
Published: March 2009

The chemokine stromal cell-derived factor-1α (SDF-1α) is a pivotal player in angiogenesis. It is capable of influencing such cellular processes as tubulogenesis and endothelial cell migration, yet very little is known about the actual signaling events that mediate SDF-1α-induced endothelial cell function. In this report, we describe the identification of an intricate SDF-1α-induced signaling cascade that involves endothelial nitric oxide synthase (eNOS), JNK3, and MAPK phosphatase 7 (MKP7). We demonstrate that the SDF-1α-induced activation of JNK3, critical for endothelial cell migration, depends on the prior activation of eNOS. Specifically, activation of eNOS leads to production of NO and subsequent nitrosylation of MKP7, rendering the phosphatase inactive and unable to inhibit the activation of JNK3. These observations reinforce the importance of nitric oxide and
S
-nitrosylation in angiogenesis and provide a mechanistic pathway for SDF-1α-induced endothelial cell migration. In addition, the discovery of this interactive network of pathways provides novel and unexpected therapeutic targets for angiogenesis-dependent diseases.
Single-round selection yields a unique retroviral envelope utilizing GPR172A as its host receptor
Authors: Mazari Peter M. , Linder-Basso Daniela , Sarangi Anindita , Chang Yehchung , Roth Monica J.
Published: March 2009

The recognition by a viral envelope of its cognate host-cell receptor is the initial critical step in defining the viral host-range and tissue specificity. This study combines a single-round of selection of a random envelope library with a parallel cDNA screen for receptor function to identify a distinct retroviral envelope/receptor pair. The 11-aa targeting domain of the modified feline leukemia virus envelope consists of a constrained peptide. Critical to the binding of the constrained peptide envelope to its cellular receptor are a pair of internal cysteines and an essential Trp required for maintenance of titers >10
5
lacZ
staining units per milliliter. The receptor used for viral entry is the human GPR172A protein, a G-protein-coupled receptor isolated from osteosarcoma cells. The ability to generate unique envelopes capable of using tissue- or disease-specific receptors marks an advance in the development of efficient gene-therapy vectors.
Social isolation alters neuroinflammatory response to stroke
Authors: Karelina Kate , Norman Greg J. , Zhang Ning , Morris John S. , Peng Haiyan , DeVries A. Courtney
Published: March 2009

Social isolation has dramatic long-term physiological and psychological consequences; however, the mechanisms by which social isolation influences disease outcome are largely unknown. The purpose of the present study was to investigate the effects of social isolation on neuronal damage, neuroinflammation, and functional outcome after focal cerebral ischemia. Male mice were socially isolated (housed individually) or pair housed with an ovariectomized female before induction of stroke, via transient intraluminal middle cerebral artery occlusion (MCAO), or SHAM surgery. In these experiments, peri-ischemic social isolation decreases poststroke survival rate and exacerbates infarct size and edema development. The social influence on ischemic damage is accompanied by an altered neuroinflammatory response; specifically, central interleukin-6 (IL-6) signaling is down-regulated, whereas peripheral IL-6 is up-regulated, in isolated relative to socially housed mice. In addition, intracerebroventricular injection of an IL-6 neutralizing antibody (10 ng) eliminates social housing differences in measures of ischemic outcome. Taken together, these data suggest that central IL-6 is an important mediator of social influences on stroke outcome.
B2 RNA and Alu RNA repress transcription by disrupting contacts between RNA polymerase II and promoter DNA within assembled complexes
Authors: Yakovchuk Petro , Goodrich James A. , Kugel Jennifer F.
Published: March 2009

Noncoding RNAs (ncRNAs) are now recognized as transregulators of eukaryotic transcription, a role once attributed exclusively to protein factors. Two ncRNAs in mammalian cells have been shown to repress general mRNA transcription by RNA polymerase II (Pol II) in response to heat shock: mouse B2 RNA and human Alu RNA. B2 and Alu RNAs bind directly and tightly to Pol II and co-occupy the promoters of repressed genes along with the polymerase. Here, we identified the molecular mechanism by which mouse B2 RNA and human Alu RNA repress Pol II transcription. Biochemical assays to probe the network of protein–DNA interactions at the promoter revealed that B2 and Alu RNAs prevent Pol II from establishing contacts with the promoter both upstream and downstream of the TATA box during closed complex formation. Disruption of these contacts correlates with transcriptional repression. We conclude that B2 and Alu RNA prevent Pol II from properly engaging the DNA during closed complex formation, resulting in complexes with an altered conformation that are transcriptionally inert. In the absence of its normal contacts with the promoter, Pol II is likely held in these inactive complexes on DNA through interactions with promoter-bound TATA box-binding protein and transcription factor IIB.
Extreme longevity in proteinaceous deep-sea corals
Authors: Roark E. Brendan , Guilderson Thomas P. , Dunbar Robert B. , Fallon Stewart J. , Mucciarone David A.
Published: March 2009

Deep-sea corals are found on hard substrates on seamounts and continental margins worldwide at depths of 300 to ≈3,000 m. Deep-sea coral communities are hotspots of deep ocean biomass and biodiversity, providing critical habitat for fish and invertebrates. Newly applied radiocarbon age dates from the deep water proteinaceous corals
Gerardia
sp. and
Leiopathes
sp. show that radial growth rates are as low as 4 to 35 μm year
−1
and that individual colony longevities are on the order of thousands of years. The longest-lived
Gerardia
sp. and
Leiopathes
sp. specimens were 2,742 years and 4,265 years, respectively. The management and conservation of deep-sea coral communities is challenged by their commercial harvest for the jewelry trade and damage caused by deep-water fishing practices. In light of their unusual longevity, a better understanding of deep-sea coral ecology and their interrelationships with associated benthic communities is needed to inform coherent international conservation strategies for these important deep-sea habitat-forming species.
A differentiation pathway for B1 cells in adult bone marrow
Authors: Esplin Brandt L. , Welner Robert S. , Zhang Qingzhao , Borghesi Lisa A. , Kincade Paul W.
Published: March 2009

The recent description of a Lin−AA4.1+CD19+B220Lo/−B1-specified progenitor (B1P) population in adult marrow adds support for the argument that these unique B cells arise from a distinct lineage. However, the origins of B1P were not investigated and their developmental relationships to conventional B2 cells remain unclear. We now report that B1P development is IL-7Rα-dependent, and negatively regulated by Bruton tyrosine kinase. Lymphoid characteristics of B1P were further studied with recombination activating gene (RAG)-1/GFP knock-in, RAG-1/Cre reporter, and VEX transgenic mice. Our results reveal that they are heterogeneous with respect to lymphocyte affiliation. RAG-1+early lymphoid progenitors and Lin−Sca-1+cKitLoIL-7Rα+common lymphoid progenitors from adult marrow efficiently generated CD19+CD45R/B220Lo/−cells in vitro and in vivo. Moreover, early lymphoid progenitors and common lymphoid progenitors produced significant numbers of peritoneal CD11b+CD5+B1a and CD11b+CD5−B1b cells in vivo. Finally, 2-step transplantation experiments established a differentiation pathway between conventional lymphoid progenitors, B1P, and mature B1 lymphocytes. Thus, our findings indicate that at least some B1P can be produced in adult bone marrow from primitive B2 progenitors, and suggest a developmental relationship between the major categories of B lymphocytes.
Starch grain and phytolith evidence for early ninth millennium B.P. maize from the Central Balsas River Valley, Mexico
Authors: Piperno Dolores R. , Ranere Anthony J. , Holst Irene , Iriarte Jose , Dickau Ruth
Published: March 2009

Questions that still surround the origin and early dispersals of maize (
Zea mays
L.) result in large part from the absence of information on its early history from the Balsas River Valley of tropical southwestern Mexico, where its wild ancestor is native. We report starch grain and phytolith data from the Xihuatoxtla shelter, located in the Central Balsas Valley, that indicate that maize was present by 8,700 calendrical years ago (cal. B.P.). Phytolith data also indicate an early preceramic presence of a domesticated species of squash, possibly
Cucurbita argyrosperma
. The starch and phytolith data also allow an evaluation of current hypotheses about how early maize was used, and provide evidence as to the tempo and timing of human selection pressure on 2 major domestication genes in
Zea
and
Cucurbita
. Our data confirm an early Holocene chronology for maize domestication that has been previously indicated by archaeological and paleoecological phytolith, starch grain, and pollen data from south of Mexico, and reshift the focus back to an origin in the seasonal tropical forest rather than in the semiarid highlands.
The mismatch repair system promotes DNA polymerase ζ-dependent translesion synthesis in yeast
Authors: Lehner Kevin , Jinks-Robertson Sue
Published: March 2009

DNA lesions that block replication can be bypassed by error-prone or error-free mechanisms. Error-prone mechanisms rely on specialized translesion synthesis (TLS) DNA polymerases that directly replicate over the lesion, whereas error-free pathways use an undamaged duplex as a template for lesion bypass. In the yeast
Saccharomyces cerevisiae
, most mutagenic TLS of spontaneous and induced DNA damage relies on DNA polymerase ζ (Polζ) activity. Here, we use a distinct mutational signature produced by Polζ in a frameshift-reversion assay to examine the role of the yeast mismatch repair (MMR) system in regulating Polζ-dependent mutagenesis. Whereas MMR normally reduces mutagenesis by removing errors introduced by replicative DNA polymerases, we find that the MMR system is required for Polζ-dependent mutagenesis. In the absence of homologous recombination, however, the error-prone Polζ pathway is not affected by MMR status. These results demonstrate that MMR promotes Polζ-dependent mutagenesis by inhibiting an alternative, error-free pathway that depends on homologous recombination. Finally, in contrast to its ability to remove mistakes made by replicative DNA polymerases, we show that MMR fails to efficiently correct errors introduced by Polζ.
Transcriptional neoteny in the human brain
Authors: Somel Mehmet , Franz Henriette , Yan Zheng , Lorenc Anna , Guo Song , Giger Thomas , Kelso Janet , Nickel Birgit , Dannemann Michael , Bahn Sabine , Webster Maree J. , Weickert Cynthia S. , Lachmann Michael , Pääbo Svante , Khaitovich Philipp
Published: March 2009

In development, timing is of the utmost importance, and the timing of developmental processes often changes as organisms evolve. In human evolution, developmental retardation, or neoteny, has been proposed as a possible mechanism that contributed to the rise of many human-specific features, including an increase in brain size and the emergence of human-specific cognitive traits. We analyzed mRNA expression in the prefrontal cortex of humans, chimpanzees, and rhesus macaques to determine whether human-specific neotenic changes are present at the gene expression level. We show that the brain transcriptome is dramatically remodeled during postnatal development and that developmental changes in the human brain are indeed delayed relative to other primates. This delay is not uniform across the human transcriptome but affects a specific subset of genes that play a potential role in neural development.
On the chimeric nature, thermophilic origin, and phylogenetic placement of the Thermotogales
Authors: Zhaxybayeva Olga , Swithers Kristen S. , Lapierre Pascal , Fournier Gregory P. , Bickhart Derek M. , DeBoy Robert T. , Nelson Karen E. , Nesbø Camilla L. , Doolittle W. Ford , Gogarten J. Peter , Noll Kenneth M.
Published: March 2009

Since publication of the first Thermotogales genome,Thermotoga maritimastrain MSB8, single- and multi-gene analyses have disagreed on the phylogenetic position of this order of Bacteria. Here we present the genome sequences of 4 additional members of the Thermotogales (Tt. petrophila,Tt. lettingae,Thermosipho melanesiensis, andFervidobacterium nodosum) and a comprehensive comparative analysis including the originalT. maritimagenome. While ribosomal protein genes strongly place Thermotogales as a sister group to Aquificales, the majority of genes with sufficient phylogenetic signal show affinities to Archaea and Firmicutes, especially Clostridia. Indeed, on the basis of the majority of genes in their genomes (including genes that are also found in Aquificales), Thermotogales should be considered members of the Firmicutes. This result highlights the conflict between the taxonomic goal of assigning every species to a unique position in an inclusive Linnaean hierarchy and the evolutionary goal of understanding phylogenesis in the presence of pervasive horizontal gene transfer (HGT) within prokaryotes. Amino acid compositions of reconstructed ancestral sequences from 423 gene families suggest an origin of this gene pool even more thermophilic than extant members of this order, followed by adaptation to lower growth temperatures within the Thermotogales.
The medial prefrontal cortex exhibits money illusion
Authors: Weber Bernd , Rangel Antonio , Wibral Matthias , Falk Armin
Published: March 2009

Behavioral economists have proposed that money illusion, which is a deviation from rationality in which individuals engage in nominal evaluation, can explain a wide range of important economic and social phenomena. This proposition stands in sharp contrast to the standard economic assumption of rationality that requires individuals to judge the value of money only on the basis of the bundle of goods that it can buy—its real value—and not on the basis of the actual amount of currency—its nominal value. We used fMRI to investigate whether the brain's reward circuitry exhibits money illusion. Subjects received prizes in 2 different experimental conditions that were identical in real economic terms, but differed in nominal terms. Thus, in the absence of money illusion there should be no differences in activation in reward-related brain areas. In contrast, we found that areas of the ventromedial prefrontal cortex (vmPFC), which have been previously associated with the processing of anticipatory and experienced rewards, and the valuation of goods, exhibited money illusion. We also found that the amount of money illusion exhibited by the vmPFC was correlated with the amount of money illusion exhibited in the evaluation of economic transactions.
COUP-TFII acts downstream of Wnt/β-catenin signal to silence PPARγ gene expression and repress adipogenesis
Authors: Okamura Masashi , Kudo Hiromi , Wakabayashi Ken-ichi , Tanaka Toshiya , Nonaka Aya , Uchida Aoi , Tsutsumi Shuichi , Sakakibara Iori , Naito Makoto , Osborne Timothy F. , Hamakubo Takao , Ito Sadayoshi , Aburatani Hiroyuki , Yanagisawa Masashi , Kodama Tatsuhiko , Sakai Juro
Published: March 2009

Wnt signaling through β-catenin and TCF maintains preadipocytes in an un-differentiated proliferative state; however, the molecular pathway has not been completely defined. By integrating gene expression microarray, chromatin immunoprecipitation-chip, and cell-based experimental approaches, we show that Wnt/β-catenin signaling activates the expression of COUP-TFII which recruits the SMRT corepressor complex to the first introns located downstream from the first exons of both PPARγ1 and γ2 mRNAs. This maintains the local chromatin in a hypoacetylated state and represses PPARγ gene expression to inhibit adipogenesis. Our experiments define the COUP-TFII/SMRT complex as a previously unappreciated component of the linear pathway that directly links Wnt/β-catenin signaling to repression of PPARγ gene expression and the inhibition of adipogenesis.