bluuebunny/crossref_metadata_2025 huggingface dataset:
High-throughput single-cell manipulation system for a large number of target cells
Authors: Arakawa Takahiro , Noguchi Masao , Sumitomo Keiko , Yamaguchi Yoshinori , Shoji Shuichi
Published: April 2011

A sequential and high-throughput single-cell manipulation system for a large volume of cells was developed and the successive manipulation for single cell involving single-cell isolation, individual labeling, and individual rupture was realized in a microhydrodynamic flow channel fabricated by using two-dimensional simple flow channels. This microfluidic system consisted of the successive single-cell handlings of single-cell isolation from a large number of cells in cell suspension, labeling each isolated single cell and the lysate extraction from each labeled single cell. This microfluidic system was composed of main channels, cell-trapping pockets, drain channels, and single-cell content collection channels which were fabricated by polydimethylsiloxane. We demonstrated two kinds of prototypes for sequential single-cell manipulations, one was equipped with 16 single-cell isolation pockets in microchannel and the other was constructed of 512 single-cell isolation pockets. In this study, we demonstrated high-throughput and high-volume single-cell isolation with 512 pocket type device. The total number of isolated single cells in each isolation pocket from the cell suspension at a time was 426 for the cell line of African green monkey kidney, COS-1, and 360 for the rat primary brown preadipocytes, BAT. All isolated cells were stained with fluorescence dye injected into the same microchannel successfully. In addition, the extraction and collection of the cell contents was demonstrated using isolated stained COS-1 cells. The cell contents extracted from each captured cell were individually collected within each collection channel by local hydrodynamic flow. The sequential trapping, labeling, and content extraction with 512 pocket type devices realized high-throughput single-cell manipulations for innovative single-cell handling, feasible staining, and accurate cell rupture.
Multimode stretched spiral vortex and nonequilibrium energy spectrum in homogeneous shear flow turbulence
Authors: Horiuti Kiyosi , Ozawa Tetsuya
Published: April 2011

The stretched spiral vortex [T. S. Lundgren, “Strained spiral vortex model for turbulent structures,” Phys. Fluids 25, 2193 (1982)] is identified in turbulence in homogeneous shear flow and the spectral properties of this flow are studied using direct-numerical simulation data. The effects of mean shear on the genesis, growth, and annihilation processes of the spiral vortex are elucidated, and the role of the spiral vortex in the generation of turbulence is shown. As in homogeneous isotropic turbulence [K. Horiuti and T. Fujisawa, “The multi mode stretched spiral vortex in homogeneous isotropic turbulence,” J. Fluid Mech. 595, 341 (2008)], multimodes of the spiral vortex are extracted. Two symmetric modes of configurations with regard to the vorticity alignment along the vortex tube in the core region and dual vortex sheets spiraling around the tube are often educed. One of the two symmetric modes is created by a conventional rolling-up of a single spanwise shear layer. Another one is created by the convergence of the recirculating flow or streamwise roll [F. Waleffe, “Homotopy of exact coherent structures in plane shear flows,” Phys. Fluids 15, 1517 (2003)] caused by the upward and downward motions associated with the streaks. The vortex tube is formed by axial straining and lowering of pressure in the recirculating region. The spanwise shear layers are entrained by the tube and they form spiral turns. The latter symmetric mode tends to be transformed into the former mode with lapse of time due to the action of the pressure Hessian term. The power law in the inertial subrange energy spectrum is studied. The base steady spectrum fits the equilibrium Kolmogorov −5/3 spectrum, to which a nonequilibrium component induced by the fluctuation of the dissipation rate ε is added. This component is extracted using the conditional sampling on ε, and it is shown that it fits the −7/3 power in accordance with the statistical theory. The correlation between these spectra and the appearance and diminution of the streaks and the two modes of the spiral vortex is discussed. The temporal variations of the spectrum are divided into two regimes, Phases 1 and 2. Large energy contained in the low-wavenumber range in Phase 1 is cascaded to the small scales in Phase 2. This energy transfer is accomplished by the reversal in the sign of −7/3 power component.
Dislocation density-dependent quality factors in InGaN quantum dot containing microdisks
Authors: El-Ella H. A. R. , Rol F. , Kappers M. J. , Russell K. J. , Hu E. L. , Oliver R. A.
Published: April 2011

Microdisks incorporating InGaN quantum dots were fabricated using SiO2 microspheres as a hard mask in conjunction with a photoelectrochemical etch step from a structure containing a sacrificial InGaN/InGaN superlattice. Formation of microdisks from two near-identical structures with differing dislocation densities was carried out and investigated using microphotoluminescence. This confirmed the existence of quantum dots through the presence of resolution limited spectral lines and showed a clear correlation between the resulting modes quality factors and the dislocation densities within the disks. The disks with higher dislocation densities showed up to 80% lower quality factors than the low dislocation density disks.
Detecting non-Maxwellian electron velocity distributions at JET by high resolution Thomson scattering
Authors: Beausang K. V. , Prunty S. L. , Scannell R. , Beurskens M. N. , Walsh M. J. , de La Luna E. ,   JET EFDA Contributors
Published: April 2011

The present work is motivated by a long standing discrepancy between the electron temperature measurements of Thomson scattering (TS) and electron cyclotron emission (ECE) diagnostics for plasmas with strong auxiliary heating observed at both JET and TFTR above 6–7 keV, where in some cases the ECE electron temperature measurements can be 15%–20% higher than the TS measurements. Recent analysis based on ECE results at JET has shown evidence of distortions to the Maxwellian electron velocity distribution and a correlation with the TS and ECE discrepancies has been suggested. In this paper, a technique to determine the presence of non-Maxwellian behavior using TS diagnostics is outlined. The difficulties and limitations of modern TS system designs to determine the electron velocity distribution are also discussed. It is demonstrated that small deviations such as those suggested by previous ECE analysis could be potentially detected, depending on the spectral layout of the TS polychromators. The spectral layout of the JET high resolution Thomson scattering system is such that it could be used to determine these deviations between 1 and 6 keV, and the results presented here indicate that no evidence of non-Maxwellian behavior is observed in this range. In this paper, a modification to the current polychromator design is proposed, allowing non-Maxwellian distortions to be detected up to at least 10 keV
Gold nanoparticle wire and integrated wire array for electronic detection of chemical and biological molecules
Authors: Diao J. J. , Cao Qing
Published: April 2011

Nanoparticle wire and integrated nanoparticle wire array have been prepared through a green technique: discontinuous vertical evaporation-driven colloidal deposition. The conducting gold nanoparticle wire made by this technique shows ability for the sensitive electronic detection of chemical and biological molecules due to its high surface to volume ratio. Furthermore, we also demonstrate a potential usage of integrated gold nanoparticle wire array for the localized detection.
Triplet states of zigzag edged hexagonal graphene molecules C6m**2H6m (m = 1, 2, 3, …, 10) and carbon based magnetism
Authors: Philpott Michael R. , Kawazoe Yoshiyuki
Published: April 2011

The geometry and magnetization (spin distribution) of the series of flat hexagonal zigzag edged molecules C6m**2H6m (m = 1,2, …, 10) in their lowest triplet state (Sz = 1) has been calculated using density functional theory and a connection established from the known benzene (m = 1) triplets to the triplets and singlet ground state of the largest molecules (m = 9, 10). The triplet state potential energy surface has two minima corresponding to distortions from the ground state geometry, such that CC bonds bisected by a \documentclass[12pt]{minimal}\begin{document}${\rm C}_{2}^{\prime \prime }$\end{document}C2″ rotation axis are either longer or shorter. For both geometries, the spin on the carbon atoms forms a pattern that peaks at the middle of an edge and for large index (m) values is the same (apart from sign) as the edge pattern of the hexagonally sectored singlet radical ground state of the largest member C600H60. This similarity suggests that the singlet ground state of the larger (m = 9, 10) zigzag edged hexangulenes is possibly a hex-radical, in some ways analogous to the di- and higher multiradical ground state of the linear acenes C4m + 2H2m + 4 starting around m ⩾ 8 and 9. The spin patterns provide guidance in interpreting the multiradical nature of ground and low lying excited states of large hexangulenes and how magnetism evolves with size in molecules with graphene cores.
Vertical conduction behavior through atomic graphene device under transverse electric field
Authors: Lee Yun-Hi , Kim Yoon-Joong , Lee J.-H.
Published: April 2011

Many studies have characterized disordered graphene layers as variable-range hopping and activated hopping conduction for a graphene structure with planar left and right electrodes. We report the electrical transport measurements of atomic-thick-graphene with top and bottom Ti/Pt electrodes. In the vertical device of metal-graphene-metal under a transverse electric field, the current at the low field or high temperature was explained by bulk-limited conduction, so called Ohmic current. On the other hand, space-charge-limited-conduction dominated at low temperatures or under high fields. The estimated trap concentration for the high field or low temperature conduction was approximately 3.7×1017 cm−3, and from a cessation of the power law dependence in the J-V characteristics it was determined that the onset of failure breakdown of the vertical GL structure began after dissipating power of 2.7×1012 W m−3.
A superconducting quantum interference device based read-out of a subattonewton force sensor operating at millikelvin temperatures
Authors: Usenko O. , Vinante A. , Wijts G. , Oosterkamp T. H.
Published: April 2011

We present a scheme to measure the displacement of a nanomechanical resonator at cryogenic temperature. The technique is based on the use of a superconducting quantum interference device to detect the magnetic flux change induced by a magnetized particle attached on the end of the resonator. Unlike conventional interferometric techniques, our detection scheme does not involve direct power dissipation in the resonator, and therefore, is particularly suitable for ultralow temperature applications. We demonstrate its potential by cooling an ultrasoft silicon cantilever to a noise temperature of 25 mK, corresponding to a subattonewton thermal force noise of 0.5 aN/Hz.
Enhanced current-induced domain wall motion by tuning perpendicular magnetic anisotropy
Authors: Emori Satoru , Beach Geoffrey S. D.
Published: April 2011

The effect of perpendicular magnetic anisotropy (PMA) on current-induced domain wall (DW) motion is investigated by micromagnetic simulations. The critical current density JC to drive DWs into periodic transformation and continuous motion by adiabatic spin transfer torque decreases with increasing PMA. Also, with optimized PMA that almost exactly compensates the demagnetizing field, the adiabatic displacement of DWs driven by currents less than JC is strongly enhanced. Since PMA can be controlled easily in magnetic multilayer films, this technique of enhancing current-induced DW motion may be practical for device applications.
Influence of binary Coulomb collisions on nonlinear stimulated Raman backscatter in the kinetic regime
Authors: Finnegan S. M. , Yin L. , Kline J. L. , Albright B. J. , Bowers K. J.
Published: April 2011

The influence of binary Coulomb collisions on trapped particle nonlinearities related to stimulated Raman scatter (SRS) in a single laser speckle is examined using one-dimensional particle-in-cell simulations. Binary Coulomb collisions are incorporated using a numerical particle-pairing algorithm that reproduces a collision integral of the Landau form. The onset of nonlinearly enhanced levels of SRS reflectivity is shown to coincide with electron trapping in the daughter plasma wave and is sensitive to the collisional scattering rate. Relaxation of trapping-induced perturbations to the electron velocity distribution via collisional velocity space diffusion is predicted to have the largest effect on the onset of SRS when the amplitude of the daughter plasma wave is smallest, and trapping-induced perturbations to the electron velocity distribution function are also small. In the absence of higher dimensional detrapping mechanisms (e.g., electron side-loss), it is shown that the onset threshold for enhanced SRS reflectivity is determined predominantly by the parallel diffusion of trapped electrons scattering from bulk thermal electrons, and that for the conditions studied here, the contribution to detrapping from perpendicular diffusion is non-negligible. Additionally, inverse bremsstrahlung heating of the bulk electrons is shown to shift the daughter plasma wave spectrum upward along the Stoke’s resonance to larger wave frequency and smaller wave number, changing the linear parametric coupling conditions to SRS backscatter as a function of time. The reduction in SRS reflectivity from binary Coulomb collisions is greatest for laser intensities near the collisionless onset threshold, ulimately leading to an increase in the onset threshold laser intensity for enhanced SRS reflectivity in the kinetic regime.
Surface-enhanced Raman scattering from silver-coated opals
Authors: Mu Weiqiang , Hwang Dae-Kue , Chang Robert P. H. , Sukharev Maxim , Tice Daniel B. , Ketterson John B.
Published: April 2011

We describe surface-enhanced Raman scattering measurements from a benzenethiol monolayer adsorbed on a silver-coated film that is, in turn, deposited on an artificial opal, where the latter is a close-packed three-dimensional dielectric lattice formed from polystyrene spheres. Data for a range of sphere sizes, silver film thicknesses, and laser excitation wavelengths are obtained. Enhancement factors can be in the range of 107. To partially explain these large enhancements, we have performed model finite-difference time domain simulations of the position-dependent electric fields generated at the opal surfaces for several experimentally studied laser wavelengths and sphere diameters.
Carrier capture delay and modulation bandwidth in an edge-emitting quantum dot laser
Authors: Asryan Levon V. , Wu Yuchang , Suris Robert A.
Published: April 2011

We show that the carrier capture from the optical confinement layer into quantum dots (QDs) can strongly limit the modulation bandwidth ω−3 dB of a QD laser. As a function of the cross-section σn of carrier capture into a QD, ω−3 dB asymptotically approaches its highest value when σn→∞ (the case of instantaneous capture). With reducing σn, ω−3 dB decreases and becomes zero at a certain nonvanishing σnmin. The use of multiple-layers with QDs significantly improves the laser modulation response—ω−3 dB is considerably higher in a multilayer structure as compared to a single-layer structure at the same dc current.
A sliding plate microgap rheometer for the simultaneous measurement of shear stress and first normal stress difference
Authors: Baik Seung Jae , Moldenaers Paula , Clasen Christian
Published: April 2011

A new generation of the “flexure-based microgap rheometer” (the N-FMR) has been developed which is also capable of measuring, in addition to the shear stress, the first normal stress difference of micrometer thin fluid films. This microgap rheometer with a translation system based on compound spring flexures measures the rheological properties of microliter samples of complex fluids confined in a plane couette configuration with gap distances of h = 1–400 μm up to shear rates of $\dot \gamma$γ̇ = 3000 s−1. Feed back loop controlled precise positioning of the shearing surfaces with response times <1 ms enables to control the parallelism within 1.5 μrad and to maintain the gap distance within 20 nm. This precise gap control minimizes squeeze flow effects and allows therefore to measure the first normal stress difference N1 of the thin film down to a micrometer gap distance, with a lower limit of ${{N_1 }/{\dot \gamma }} = 9.375 \times 10^{ - 11} {\eta/{h^2 }}$N1/γ̇=9.375×10−11η/h2 that depends on the shear viscosity η and the squared inverse gap. Structural development of complex fluids in the confinement can be visualized by using a beam splitter on the shearing surface and a long working distance microscope. In summary, this new instrument allows to investigate the confinement dependent rheological and morphological evolution of micrometer thin films.
Fast frequency-resolved terahertz imaging
Authors: Yasuda Takashi , Kawada Yoichi , Toyoda Haruyoshi , Nakanishi Atsushi , Akiyama Koichiro , Takahashi Hironori
Published: April 2011

We propose a fast, frequency-resolved, real-time, terahertz imaging method. With our method, images at two specific terahertz frequencies can be acquired in 1 min. Three kinds of drugs (L-histidine, maltose, and CBZ3), which have absorption peaks in the terahertz region, were distinguished in 3 min by using our method. This technique can be used in industrial applications, such as nondestructive testing.
Nondestructive estimation of depletion layer profile in Nb-doped SrTiO3/(La,Ba)MnO3 heterojunction diode structure by hard x-ray photoemission spectroscopy
Authors: Tanaka Hidekazu , Satoh Issei , Kanki Teruo , Ikenaga Eiji , Kobata Masaaki , Kim Jung Jin , Ueda Shigenori , Kobayashi Keisuke
Published: April 2011

We report the hard x-ray (hv=7.94 keV) core level photoemission spectroscopy to determine the depletion layer profile in Nb-doped SrTiO3/(La,Ba)MnO3 n-p+ diode structures. The Sr 2p3/2 spectra were detected penetrating even through (La,Ba)MnO3 over layer with thickness of 20 nm. The spectrum for a 0.01 wt % Nb doped SrTiO3 diode exhibited large shift to lower binding energy, whereas the spectrum for a 0.5 wt % Nb doped SrTiO3 diode exhibited small shift with broader width. The depletion layer lengths were experimentally estimated as 182 nm for 0.01 wt % one and 15 nm for 0.5 wt % one, respectively, in good agreement with semiconductor theory.
Supernatant decanting on a centrifugal platform
Authors: Shih Chih-Hsin , Lu Chien-Hsing , Yuan Wei-Li , Chiang Wei-Ling , Lin Chia-Hui
Published: April 2011

This study presents a novel approach to decant supernatant on a centrifugal platform. By manipulating the centrifugally induced pressure and the elastic deformation of the plastic lids in the decanting chamber, fixed amounts of the supernatant can be decanted into the detection chamber at lower rotational speeds. The experimental results showed that decanted volume is affected by the volume of deformation and the operating parameters. Factors that influence the decanting ratio are also discussed. This approach has the advantages of simple design and low manufacturing cost; further, it has no need of surface modification. It has been applied to on-disk separation of plasma from whole blood, and the results showed good stability and repeatability.
Preface to Special Topic: Biological microfluidics in tissue engineering and regenerative medicine
Authors: Jayasinghe Suwan N.
Published: April 2011

In this special issue of Biomicrofluidics, many manifestations of biological microfluidics have been highlighted that have significance to regenerative biology and medicine. The collated articles demonstrate the applicability of these biological microfluidics for studying a wide range of biomedical problems most useful for understanding and shining light on basic biology to those applications relevant to clinical medicine.
Linear dichroism amplification: Adapting a long-known technique for ultrasensitive femtosecond IR spectroscopy
Authors: Réhault Julien , Zanirato Vinicio , Olivucci Massimo , Helbing Jan
Published: April 2011

We demonstrate strong amplification of polarization-sensitive transient IR signals using a pseudo-null crossed polarizer technique first proposed by Keston and Lospalluto [Fed. Proc. 10, 207 (1951)] and applied for nanosecond flash photolysis in the visible by Che et al. [Chem. Phys. Lett. 224, 145 (1994)]. We adapted the technique to ultrafast pulsed laser spectroscopy in the infrared using photoelastic modulators, which allow us to measure amplified linear dichroism at kilohertz repetition rates. The method was applied to a photoswitch of the N-alkylated Schiff base family in order to demonstrate its potential of strongly enhancing sensitivity and signal to noise in ultrafast transient IR experiments, to simplify spectra and to determine intramolecular transition dipole orientations.
One-step synthesis of titanium oxide with trilayer structure for dye-sensitized solar cells
Authors: Liu Meinan , Wang Hongxia , Yan Cheng , Will Geoffrey , Bell John
Published: April 2011

Titanium oxide films with trilayer structure grown on fluorine doped tin oxide substrate were prepared from one-step hydrothermal process. The trilayer structure consists of microflowers, nanorod array and compact nanoparticulates, which is expected to possess the merits of good light harvesting, a high electron transport rate, while avoiding the issues of electron shunting. The photovoltaic performance was comprehensively studied and a 60% enhancement in short circuit photocurrent density was found from microflowers contribution as a light scattering layer. This unique trilayer structure exhibits great potential application in future dye-sensitized solar cells.
Static charging of graphene and graphite slabs
Authors: Topsakal M. , Ciraci S.
Published: April 2011

The effect of external static charging of graphene and its flakes are investigated by using first-principles calculations. While the Fermi level of negatively charged graphene rises and then is quickly pinned by the parabolic, nearly free electronlike bands, it moves down readily by removal of electrons from graphene. Excess charges accumulate mainly at both surfaces of graphite slab. Even more remarkable is that Coulomb repulsion exfoliates the graphene layers from both surfaces of positively charged graphite slab. The energy level structure, binding energy, and spin-polarization of specific adatoms adsorbed to a graphene flake can be monitored by charging.
Vacancy induced metallicity at the CaHfO3/SrTiO3 interface
Authors: Nazir S. , Pulikkotil J. J. , Singh N. , Schwingenschlögl U.
Published: April 2011

Density functional theory is used to study the electronic properties of the oxide heterointerface CaHfO3/SrTiO3. Structural relaxation is carried out with and without O vacancies. As compared to related interfaces, strongly reduced octahedral distortions are found. Stoichiometric interfaces between the wide band gap insulators CaHfO3 and SrTiO3 turn out to exhibit an insulating state. However, interface metallicity is introduced by O vacancies, in agreement with experiment. The reduced octahedral distortions and necessity of O deficiency indicate a less complicated mechanism for the creation of the interfacial electron gas.
Introduction of a dc bias into a high-Q superconducting microwave cavity
Authors: Chen Fei , Sirois A. J. , Simmonds R. W. , Rimberg A. J.
Published: April 2011

We report a technique for applying a dc voltage or current bias to the center conductor of a high-quality factor superconducting microwave cavity without significantly disturbing selected cavity modes. This is accomplished by incorporating dc bias lines into the cavity at specific locations. The measured S-matrix parameters of the system are in good agreement with theoretical predictions and simulations. We find that at 4 K the quality factor of the cavity degrades by less than 1% under the application of a dc bias.
Continuous roll-to-roll growth of graphene films by chemical vapor deposition
Authors: Hesjedal Thorsten
Published: April 2011

Few-layer graphene is obtained in atmospheric chemical vapor deposition on polycrystalline copper in a roll-to-roll process. Raman and x-ray photoelectron spectroscopy were employed to confirm the few-layer nature of the graphene film, to map the inhomogeneities, and to study and optimize the growth process. This continuous growth process can be easily scaled up and enables the low-cost fabrication of graphene films for industrial applications.
Nanofabricated solid immersion lenses registered to single emitters in diamond
Authors: Marseglia L. , Hadden J. P. , Stanley-Clarke A. C. , Harrison J. P. , Patton B. , Ho Y.-L. D. , Naydenov B. , Jelezko F. , Meijer J. , Dolan P. R. , Smith J. M. , Rarity J. G. , O’Brien J. L.
Published: April 2011

We describe a technique for fabricating micro- and nanostructures incorporating fluorescent defects in diamond with a positional accuracy better than hundreds of nanometers. Using confocal fluorescence microscopy and focused ion beam etching, we initially locate a suitable defect with respect to registration marks on the diamond surface then etch a structure using these coordinates. We demonstrate the technique by etching an 8 μm diameter hemisphere positioned with single negatively charged nitrogen-vacancy defect lies at its origin. Direct comparison of the fluorescence photon count rate before and after fabrication shows an eightfold increase due to the presence of the hemisphere.
Large magnetoelectric effect in mechanically mediated structure of TbFe2, Pb(Zr,Ti)O3, and nonmagnetic flakes
Authors: Bi K. , Wang Y. G. , Pan D. A. , Wu W.
Published: April 2011

Magnetoelectric (ME) effect has been studied in a structure of a magnetostrictive TbFe2 alloy, two piezoelectric Pb(Zr,Ti)O3 (PZT) ceramics, and two nonmagnetic flakes. The ME coupling originates from the magnetic-mechanical-electric transform of the magnetostrictive effect in TbFe2 and the piezoelectric effect in PZT by end bonding, instead of interface bonding. Large ME coefficients of 10.5 and 9.9 V cm−1 Oe−1 were obtained at the first planar acoustic and third bending resonance frequencies, which are larger than that of conventional layered TbFe2/PZT composites. The results show that the large ME coupling can be achieved without interface coupling.
The dielectric suppress and the control of semiconductor non-Ohmic feature of CaCu3Ti4O12 by means of tin doping
Authors: Ribeiro Willian C. , Araújo Rafael G. C. , Bueno Paulo R.
Published: April 2011

In this work it was demonstrated that the addition of Sn on CaCu3Ti4O12 material improved non-Ohmic behavior by suppressing dielectric properties. It was noted that the improvement of the varistor characteristics, monitored by the increase in nonlinear coefficient, occurs with the disappearance of the grain dielectric relaxation process with concomitant decreasing of both dielectric constant and dielectric loss values. By forming a solid solution, Sn4+ was incorporated into CaCu3Ti4O12 matrix deforming the crystal lattice and restricting the formation of polaronic stacking faults. Thus, the dielectric relaxation due to polaronic defects is believed to be the origin of the huge dielectric properties disappearance. This framework is in agreement with the nanosized barrier layer capacitor model.
Molecular dynamics simulations of vapor/liquid coexistence using the nonpolarizable water models
Authors: Sakamaki Ryuji , Sum Amadeu K. , Narumi Tetsu , Yasuoka Kenji
Published: April 2011

The surface tension, vapor–liquid equilibrium densities, and equilibrium pressure for common water models were calculated using molecular dynamics simulations over temperatures ranging from the melting to the critical points. The TIP4P/2005 and TIP4P-i models produced better values for the surface tension than the other water models. We also examined the correlation of the data to scaling temperatures based on the critical and melting temperatures. The reduced temperature (T/Tc) gives consistent equilibrium densities and pressure, and the shifted temperature T + (Tc, exp − Tc, sim) gives consistent surface tension among all models considered in this study. The modified fixed charge model which has the same Lennard-Jones parameters as the TIP4P-FQ model but uses an adjustable molecular dipole moment is also simulated to find the differences in the vapor–liquid coexistence properties between fixed and fluctuating charge models. The TIP4P-FQ model (2.72 Debye) gives the best estimate of the experimental surface tension. The equilibrium vapor density and pressure are unaffected by changes in the dipole moment as well as the surface tension and liquid density.
Aluminum plasmonic nanostructures for improved absorption in organic photovoltaic devices
Authors: Kochergin Vladimir , Neely Lauren , Jao Chih-Yu , Robinson Hans D.
Published: April 2011

We model the absorption enhancement in organic photovoltaic devices induced by incorporating Al, Ag, and Au nanoparticles in the active layer. We find that Al nanoparticles should yield significantly greater enhancement than Ag or Au. This is because the much higher plasma frequency of Al ensures a better overlap between plasmon resonance and absorption band of organic semiconductors. Our predictions are verified experimentally by demonstrating enhanced absorbance in a poly(3-hexylthiophene-2,5-diyl): [6,6]-phenyl C61 butyric acid methyl ester layer with embedded functionalized Al nanoparticles.
Intermixing between HfO2 and GeO2 films deposited on Ge(001) and Si(001): Role of the substrate
Authors: Soares G. V. , Krug C. , Miotti L. , Bastos K. P. , Lucovsky G. , Baumvol I. J. R. , Radtke C.
Published: April 2011

Thermally driven atomic transport in HfO2/GeO2/substrate structures on Ge(001) and Si(001) was investigated in N2 ambient as function of annealing temperature and time. As-deposited stacks showed no detectable intermixing and no instabilities were observed on Si. On Ge, loss of O and Ge was detected in all annealed samples, presumably due to evolution of GeO from the GeO2/Ge interface. In addition, hafnium germanate is formed at 600 °C. Our data indicate that at 500 °C and above HfO2/GeO2 stacks are stable only if isolated from the Ge substrate.
Coherent phonons in bismuth film observed by ultrafast electron diffraction
Authors: Bugayev A. , Esmail A. , Abdel-Fattah M. , Elsayed-Ali H. E.
Published: April 2011

The generation of coherent phonons in polycrystalline bismuth film excited with femtosecond laser pulse is observed by ultrafast time-resolved electron diffraction. The dynamics of the diffracted intensities from the (110), (202), and (024) lattice planes show pronounced oscillations at 130–150 GHz. The origin of these coherent acoustic phonons is discussed in view of optical phonon decay into two acoustic phonons. Different drop times in the intensity of the diffraction orders are observed and interpreted as anisotropy in the energy transfer rate of coherent optical phonons.
Effects of substrate-blocks interactions on the phase behaviors of cylinder-forming block copolymers
Authors: Park Dongsik , Sancaktar Erol
Published: April 2011

Self-assembly of block copolymers greatly facilitates production of controlled periodic nanostructures for nanotechnological applications. Orientation control in such structures with defect-free ordering on larger length scales still remain a major research challenge in many cases. In addition to their pure block forms, blends of copolymers with other polymers offer productive research areas in relation to nanostructure self-assembly. We prepared well-aligned nanocylinders in block copolymers over an enhanced sample area and height scale without using any external field applications. Self-assembled 3-dimensional perpendicular cylinder orientation was achieved mainly by blending of minority homopolymer into the block copolymer. In this work, we illustrate that the mixed cylinder nanodomain orientation exits in block copolymer mixtures even with a relatively strong homologous polymer pair interaction and a decreased domain-domain excess free energy, when the interfacial interaction between the majority component and the substrate is high enough to restrict the perpendicular nanodomain orientation. In case of overall perpendicular cylinder-forming block copolymer mixtures, on the other hand, the strong homologous PS pair interaction overcomes the limitation from the relatively high domain-substrate interfacial interactions.
Trefoil factor 1 acts to suppress senescence induced by oncogene activation during the cellular transformation process
Authors: Radiloff Daniel R. , Wakeman Timothy P. , Feng Junjie , Schilling Stephen , Seto Edward , Wang Xiao-Fan
Published: March 2011

Senescence is a cellular stress response characterized by persistent cell growth arrest under various stress conditions, including oncogene activation or tumor suppressor loss, which functions as a critical barrier that must be overcome to allow the progression from a precancerous or preinvasive lesion to a malignant tumor. Trefoil factor 1 (TFF1) is a secreted protein involved in maintaining the gastrointestinal epithelium by serving a tumor-suppressive role; however, TFF1 is overexpressed in several types of cancers. Here we report that TFF1 acts as a promoter of tumorigenesis in the context of prostate and pancreatic cancers by suppressing oncogene-induced senescence (OIS). Expression of TFF1 allows human prostate epithelial cells to escape OIS caused by the activated Ras oncogene or by reduced expression of the tumor suppressor PTEN, in part by the involvement of the EGF receptor-mediated pathway and inhibition of the expression of the cell cycle regulator p21. Without intrinsic promitogenic activity TFF1 may act in both autocrine and paracrine manners to enable cells to undergo the initial transformation and expansion against the restrictive microenvironment during early stage tumorigenesis. Taken together, our findings identify TFF1 as a soluble factor designed to act mainly to antagonize the OIS process to accelerate tumorigenesis.
Tradeoffs in the Policy Process in Advancing Climate Change Adaptation: The Case of Australia's Great Eastern Ranges Initiative
Authors: Levin Kelly , Petersen Brian
Published: April 2011

The first continental-scale climate change adaptation strategy for biodiversity conservation has been adopted in Australia. The Great Eastern Ranges Initiative (GERI), aims to bolster the resilience of biodiversity by enhancing connectivity in eastern Australia for species migration in a changing climate. The Initiative is now being carried out on the ground, and is among the earliest national-level adaptation strategies for biodiversity conservation advanced by policymakers. In this paper we explore the implications of the rapid progression of the Initiative through the policy process, providing insights useful for decision makers advancing adaptation policies elsewhere in the future.
Cooperation Across Boundaries: The Role of Political Entrepreneurs in Environmental Collaboration
Authors: Schoon Michael L. , York Abigail M.
Published: April 2011

This paper links disparate scholarship in cross-border environmental institutions from local and global policymaking literature. We explore the ability of political entrepreneurs to broker deals across borders utilizing game theory as a metaphor for the strategic agency of the policy-making entrepreneurs. Our intent is to understand why collaboration occurs across jurisdictional boundaries in some situations and not in others and when cross-border governance works. Based on the literature, we propose and examine the explanatory power of three conditions for successful cross-border environmental negotiations: i) a skilled entrepreneur, ii) costs and benefits that are perceived as equitable, and iii) veto players' preference points (the desired end goals of the governments that the entrepreneurs represent) that are close. We use two cases to demonstrate that policy change literature can be integrated with game theoretic literature to understand game switching by political entrepreneurs in the pursuit of cross-border collaborative governance.
Miombo Woodland Utilization and Management, and Impact Perception among Stakeholders in Zambia: A Call for Policy Change in Southern Africa
Authors: Syampungani Stephen , Geldenhuys Coert J. , Chirwa Paxie W
Published: April 2011

Miombo woodland is important for both wood and non-timber forest products (NTFPs). The most commonly harvested products are timber, firewood, charcoal, fencing materials and materials for making farm tools and household items. The non-timber forest products harvested include mushrooms, fruits, medicines etc. A range of user groups such as timber producers, farmers and charcoal producers are involved in the exploitation of different types of woodland resources. Differences in priority of wood products and poor understanding of the Miombo ecosystem often result in each group attributing the negative impacts on the woodland to the other groups. In particular, timber producers accuse the charcoal producers of causing the depletion/decline of the timber species population which are cut as a by-product of charcoal production. However, there is clear evidence suggesting that timber species tend to do better in charcoal production and areas opened up due to slash and burn. This suggests that charcoal production, slash and burn agriculture and timber production may be integrated in forest management. As a result, there is need to formulate policies that provide for the integration of these different land use types into forest management.
hmChIP: a database and web server for exploring publicly available human and mouse ChIP-seq and ChIP-chip data
Authors: Chen Li , Wu George , Ji Hongkai
Published: March 2011

Summary: hmChIP is a database of genome-wide chromatin immunoprecipitation (ChIP) data in human and mouse. Currently, the database contains 2016 samples from 492 ChIP-seq and ChIP-chip experiments, representing a total of 170 proteins and 11 069 914 protein–DNA interactions. A web server provides interface for database query. Protein–DNA binding intensities can be retrieved from individual samples for user-provided genomic regions. The retrieved intensities can be used to cluster samples and genomic regions to facilitate exploration of combinatorial patterns, cell-type dependencies, and cross-sample variability of protein–DNA interactions.

Availability:  http://jilab.biostat.jhsph.edu/database/cgi-bin/hmChIP.pl

Contact:  hji@jhsph.edu

Supplementary Information:  Supplementary data are available at Bioinformatics online.
Evaluation of MP4OX for Prevention of Perioperative Hypotension in Patients Undergoing Primary Hip Arthroplasty with Spinal Anesthesia
Authors: Olofsson Christina I. , Górecki Andrzej Z. , Dirksen Ris , Kofranek Ivo , Majewski Jacek A. , Mazurkiewicz Tomasz , Jahoda David , Fagrell Bengt , Keipert Peter E. , Hardiman Yun J. , Levy Howard
Published: March 2011

Background

MP4OX (oxygenated polyethylene glycol-modified hemoglobin) is an oxygen therapeutic agent with potential applications in clinical settings where targeted delivery of oxygen to ischemic tissues is required. The primary goal of this study was to investigate MP4OX for preventing hypotensive episodes. An additional goal was to establish the safety profile of MP4OX in a large surgical population.

Methods

Patients (n = 367) from 18 active study sites in six countries, undergoing elective primary hip arthroplasty with spinal anesthesia, were randomized to receive MP4OX or hydroxyethyl starch 130/0.4. Patients received a 250-ml dose at induction of spinal anesthesia and a second 250-ml dose if the protocol-specified trigger (predefined decrease in systolic blood pressure) was reached. The primary end point was the proportion of patients who developed one or more hypotensive episodes.

Results

The proportion of patients with one or more hypotensive episodes was significantly lower (P < 0.0001) in the MP4OX group (66.1%) versus controls receiving hydroxyethyl starch 130/0.4 (90.2%). More MP4OX-treated patients experienced adverse events compared with controls (72.7% vs. 61.4%; P = 0.026). Transient elevations in laboratory values (e.g., alanine aminotransferase, aspartate aminotransferase, lipase, and troponin concentrations) occurred more frequently in the MP4OX group. There were no significant differences in the incidence of serious adverse events or in the composite morbidity and ischemia outcome end points, but nausea and hypertension were reported more often in MP4OX-treated patients.

Conclusion

MP4OX significantly reduced the incidence of hypotensive episodes in patients undergoing hip arthroplasty, but the adverse event profile does not support use in routine low-risk surgical patients for the indication evaluated in this study.
A novel antimicrobial peptide significantly enhances acid-induced killing of Shiga toxin-producing Escherichia coli O157 and non-O157 serotypes
Authors: Lino M. , Kus J. V. , Tran S. L. , Naqvi Z. , Binnington B. , Goodman S. D. , Segall A. M. , Barnett Foster D.
Published: April 2011

Shiga toxin-producing Escherichia coli (STEC) colonizes the human intestine, causing haemorrhagic colitis and haemolytic uraemic syndrome (HUS). Treatment options are limited to intravenous fluids in part because sublethal doses of some antibiotics have been shown to stimulate increased toxin release and enhance the risk of progression to HUS. Preventative antimicrobial agents, especially those that build on the natural antimicrobial action of the host defence, may provide a better option. In order to survive the acid stress of gastric passage, STEC is equipped with numerous acid resistance and DNA repair mechanisms. Inhibition of acid-induced DNA repair may offer a strategy to target survival of ingested STEC. We report here that brief pretreatment with a novel antimicrobial peptide, which was previously shown to inhibit bacterial DNA repair, significantly and profoundly reduces survival of acid-stressed O157 : H7 and non-O157 : H7 STEC seropathotypes that are highly associated with HUS. Reduction in survival rates of STEC range from 3 to 5 log. We also show that peptide/acid treatment results in little or no increase in toxin production, thereby reducing the risk of progression to HUS. This study identifies the peptide wrwycr as a potential new candidate for a preventative antimicrobial for STEC infection.
The super elongation complex (SEC) and MLL in development and disease
Authors: Smith Edwin , Lin Chengqi , Shilatifard Ali
Published: April 2011

Transcriptional regulation at the level of elongation is vital for the control of gene expression and metazoan development. The mixed lineage leukemia (MLL) protein and its Drosophila homolog, Trithorax, which exist within COMPASS (complex of proteins associated with Set1)-like complexes, are master regulators of development. They are required for proper homeotic gene expression, in part through methylation of histone H3 on Lys 4. In humans, the MLL gene is involved in a large number of chromosomal translocations that create chimeric proteins, fusing the N terminus of MLL to several proteins that share little sequence similarity. Several frequent translocation partners of MLL were found recently to coexist in a super elongation complex (SEC) that includes known transcription elongation factors such as eleven-nineteen lysine-rich leukemia (ELL) and P-TEFb. Importantly, the SEC is required for HOX gene expression in leukemic cells, suggesting that chromosomal translocations involving MLL could lead to the overexpression of HOX and other genes through the involvement of the SEC. Here, we review the normal developmental roles of MLL and the SEC, and how MLL fusion proteins can mediate leukemogenesis.
Genome-wide analysis of 5-hydroxymethylcytosine distribution reveals its dual function in transcriptional regulation in mouse embryonic stem cells
Authors: Wu Hao , D'Alessio Ana C. , Ito Shinsuke , Wang Zhibin , Cui Kairong , Zhao Keji , Sun Yi Eve , Zhang Yi
Published: April 2011

Recent studies have demonstrated that the Ten-eleven translocation (Tet) family proteins can enzymatically convert 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC). While 5mC has been studied extensively, little is known about the distribution and function of 5hmC. Here we present a genome-wide profile of 5hmC in mouse embryonic stem (ES) cells. A combined analysis of global 5hmC distribution and gene expression profile in wild-type and Tet1-depleted ES cells suggests that 5hmC is enriched at both gene bodies of actively transcribed genes and extended promoter regions of Polycomb-repressed developmental regulators. Thus, our study reveals the first genome-wide 5hmC distribution in pluripotent stem cells, and supports its dual function in regulating gene expression.
The DEK oncoprotein is a Su(var) that is essential to heterochromatin integrity
Authors: Kappes Ferdinand , Waldmann Tanja , Mathew Veena , Yu Jindan , Zhang Ling , Khodadoust Michael S. , Chinnaiyan Arul M. , Luger Karolin , Erhardt Sylvia , Schneider Robert , Markovitz David M.
Published: April 2011

Heterochromatin integrity is crucial for genome stability and regulation of gene expression, but the factors involved in mammalian heterochromatin biology are only incompletely understood. Here we identify the oncoprotein DEK, an abundant nuclear protein with a previously enigmatic in vivo function, as a Suppressor of Variegation [Su(var)] that is crucial to global heterochromatin integrity. We show that DEK interacts directly with Heterochromatin Protein 1 α (HP1α) and markedly enhances its binding to trimethylated H3K9 (H3K9me3), which is key for maintaining heterochromatic regions. Loss of Dek in Drosophila leads to a Su(var) phenotype and global reduction in heterochromatin. Thus, these findings show that DEK is a key factor in maintaining the balance between heterochromatin and euchromatin in vivo.
Preparation of Postimplantation Mouse Embryos for Imaging: Figure 1.
Authors: Garcia Monica D. , Udan Ryan S. , Hadjantonakis Anna-Katerina , Dickinson Mary E.
Published: April 2011

INTRODUCTION

Genetic manipulation methods allow fluorescent labeling of virtually any cell type or protein of interest in developing embryos, providing powerful insights into morphogenetic events at cellular and subcellular resolutions. The development of ex vivo embryo culture methods combined with high-resolution imaging provides a strong platform for observing morphogenetic events as they occur within the developing embryo. This protocol details the dissection and immobilization of postimplantation mouse embryos in preparation for live imaging.
Construction and Expression of Tetracysteine-Tagged Proteins for FlAsH-FALI
Authors: Habets Ron L.P. , Verstreken Patrik
Published: April 2011

INTRODUCTION

Fluorescein-assisted light inactivation (FALI) is a powerful method for studying acute loss of protein function, even if the corresponding mutations lead to early lethality. In this protocol, FALI is mediated by the membrane-permeable FlAsH (4′,5′-bis(1,3,2-dithioarsolan-2-yl)fluorescein) compound that binds with high specificity to the genetically encoded tetracysteine tag and thus allows the inactivation of protein function in vivo with exquisite spatial (<40 Å) and temporal (<30 sec) resolution. It also enables the analysis of kinetically distinct processes such as synaptic vesicle exocytosis and endocytosis. This protocol describes the creation of a tetracysteine-tagged construct that can be used in FlAsH-FALI. These tagged genomic constructs are cloned in a conditional amplifiable bacterial artificial chromosome (BAC), such as P(acman), using recombineering.