bluuebunny/crossref_metadata_2025 huggingface dataset:
A Tool and Index to Assess Surgical Capacity in Low Income Countries: An Initial Implementation in Sierra Leone
Authors: Groen Reinou S. , Kamara Thaim B. , Dixon‐Cole Richmond , Kwon Steven , Kingham T. Peter , Kushner Adam L.
Published: April 2012

Background

A first step toward improving surgical care in many low and middle income countries is to document the need. To facilitate the collection and analysis of surgical capacity data and measure changes over time, Surgeons OverSeas (SOS) developed a tool and index based on personnel, infrastructure, procedures, equipment, and supplies (PIPES).

Methods

A follow‐up assessment of 10 government hospitals in Sierra Leone was completed 42 months after an initial survey in 2008 using the PIPES tool. An index based on number of operating rooms, personnel, infrastructure, procedures, equipment, and supplies was calculated. An index was also calculated, using the 2008 data for comparison.

Results

Most hospitals demonstrated an increased index that correlated with site visits that verified improved conditions. Connaught Hospital in Sierra Leone had the highest score (9.2), consistent with its being the best equipped and staffed Ministry of Health and Sanitation facility. Makeni District Hospital had the greatest increase, from 3.8 to 7.5, consistent with a newly constructed facility.

Discussion

The PIPES tool was easily administered at hospitals in Sierra Leone and an index was found useful. Surgical capacity in Sierra Leone improved between 2008 and 2011, as demonstrated by an increase in the overall PIPES indices.
Effect of Mixed Nanobubble and Microbubble Liquids on the Washing Rate of Cloth in an Alternating Flow
Authors: Ushida Akiomi , Hasegawa Tomiichi , Takahashi Naoyuki , Nakajima Toshiyuki , Murao Shotaro , Narumi Takatsune , Uchiyama Hiroshige
Published: April 2012

It is well‐known that laundry waste water contributes to water pollution, and the need to reduce the amount of detergent used is widely recognized. Predominantly, research has focused on the washing effects of microbubbles and nanobubbles, and mechanical work was found to account for about 50 % of the washing effect on the cloth. In the present research, mixed nanobubble and microbubble water and four types of surfactants (including a commercial cleaning liquid) were investigated in an alternating flow system. The nanobubble water achieved a washing rate greater than that of ion‐exchanged water. However, the microbubble water had the same washing rate as ion‐exchanged water. Moreover, nanobubbles mixed with an aqueous solution of surfactant exhibited a washing rate that depended on the ionization of the surfactant: the mixture with nanobubbles and anionic surfactant exhibited a washing rate that was higher than that of aqueous anionic surfactant solution without nanobubbles. The surface tensions of nanobubble water and mixed nanobubble anionic surfactant were lower than those without nanobubble, respectively. Also, there was no advantage in mixed microbubble liquids. These results provide evidence of an enhanced washing effect by nanobubble mixtures in liquids.
Effect of polyvinylpyrrolidone on sperm function and early embryonic development following intracytoplasmic sperm injection in human assisted reproduction
Authors: Kato Yoku , Nagao Yoshikazu
Published: April 2012

The objective here was to review the effects of polyvinylpyrrolidone (PVP) upon sperm function and embryonic development in humans. PVP has been used successfully in intracytoplasmic sperm injection (ICSI) to facilitate the handling and immobilization of sperm for both domestic animals and humans. In our previous reports, PVP solution exists locally in embryos injected during the early developmental period, and also exerts influence over the developmental capacity of such embryos. In other reports, PVP causes significant damage to sperm membranes that can be detected by transmission electron microscopy, and has been associated with chromosomal abnormalities in pregnancy derived from ICSI embryos. In some Japanese clinics, PVP‐free media has been used for sperm immobilization in order to optimise safety. Consequently, it is strongly suggested that the success rate of fertilization and clinical pregnancy could be improved by using PVP‐free solution for human ICSI. In conclusion, our interpretation of the available data is to perform ICSI without PVP or select a lower concentration of PVP solution in order to reduce safety for pregnancy and children born via ICSI.
Religious Organizations and Homosexuality: The Acceptance of Gays and Lesbians in American Congregations
Authors: Whitehead Andrew L.
Published: April 2012

The participation of gays and lesbians in all aspects of society is continually disputed in the United States. Religion is one of the key battlegrounds. The extent to which religious congregations include lesbians and gays in congregational life is vital to the wider debate over homosexuality because congregations consistently influence more Americans than any other voluntary social institution reported by Putnam (Bowling alone: the collapse and revival of American community, Simon and Schuster, New York, 2000 ). Using nationally representative data from the 2006–2007 National Congregations Study this analysis investigates the level of acceptance of gays and lesbians within congregations as well as which congregations are most likely to allow lesbians and gays to become involved. I find that religious tradition, theological and political ideology, location, and demographic composition of congregations all influence the degree to which gays and lesbians are included into congregational life.
Dynamics of TGF‐β/Smad signaling
Authors: Zi Zhike , Chapnick Douglas A. , Liu Xuedong
Published: April 2012

The physiological responses to TGF‐β stimulation are diverse and vary amongst different cell types and environmental conditions. Even though the principal molecular components of the canonical and the non‐canonical TGF‐β signaling pathways have been largely identified, the mechanism that underlies the well‐established context dependent physiological responses remains a mystery. Understanding how the components of TGF‐β signaling function as a system and how this system functions in the context of the global cellular regulatory network requires a more quantitative and systematic approach. Here, we review the recent progress in understanding TGF‐β biology using integration of mathematical modeling and quantitative experimental analysis. These studies reveal many interesting dynamics of TGF‐β signaling and how cells quantitatively decode variable doses of TGF‐β stimulation.
On estimating functional average breakthrough curve using time‐warping technique and perturbation approach
Authors: Lu Zhiming , Stauffer Philip H.
Published: April 2012

Simulated contaminant breakthrough curves (BTC) are often used to predict mass arrival at compliance boundaries at waste storage sites. In numerical simulations that involve uncertainties on input parameters such as randomly heterogeneous rock properties, Monte Carlo simulations are commonly utilized and the mean breakthrough curve is often calculated from the arithmetic average of all realizations. The arithmetic mean breakthrough curve in general overestimates the mass flow rate at early and late time but underestimates the peak mass flow rate. The averaged breakthrough curve usually does not resemble any of individual breakthrough curves. The reason is that BTCs vary not only on amplitude but also on dynamics (time) and therefore it is not appropriate to take the arithmetic average directly. In this study, we consider each BTC as a random curve, and use time‐warping techniques to align all curves in a time‐warped space, compute the sample mean of the curves in the time‐warped space, and transform the means back to the original time space. We show that all BTCs are aligned based on the percentile of mass reaching the compliance boundary, and the functional average is the percentile average of all BTCs. The confidence interval of the sample mean curve is estimated using the perturbation approach. The functional average provides an additional metric that can be used to characterize the breakthrough behavior in addition to more traditional median and arithmetic average curves. The method is illustrated using transport simulations at the Material Disposal Area G, Los Alamos National Laboratory (LANL) in New Mexico.
A network of weather camps to engage students in science
Authors: Morris Vernon R. , Mogil H. Michael , Yu Tsann‐Wang
Published: April 2012

Of the total U.S. population, 12.8% are African Americans, 16.3% are Hispanic Americans, and 1.1% are Pacific Islanders, Native Americans, and Alaska Natives based on the 2010 census. Although they form about 6%, 4.5%, and 3.2%, respectively, of the total student population entering Title IV colleges and universities each year, recent statistics on underrepresented minority (URM) students show that African Americans, Hispanic Americans, and Native Americans earn only 2.1%, 3.3%, and 0.6%, respectively, of the Ph.D. degrees awarded annually in the physical sciences [National Academies Press, 2010]. A report issued by AGU and the American Geosciences Institute (AGI) reported that ethnic minorities earned fewer than 4% of the Ph.D.s in geosciences over the prior 5 years [AGI, 2009]. The report also stated that in the past 31 years combined (1973–2003) only 313 Hispanic Americans, 135 African Americans, and 49 Native Americans earned Ph.D.s in any of the geoscience fields, including Earth, atmospheric, and oceanic sciences.
What is monthly mean land surface air temperature?
Authors: Zeng Xubin , Wang Aihui
Published: April 2012

Land surface air temperature is one of the fundamental variables in weather and climate observations, modeling, and applications. Its monthly mean has been computed as the average of daily maximum and minimum temperatures [Jones et al., 1999]. This is different from the true monthly mean temperature, which is defined as the integral of the continuous temperature measurements in a month divided by the integration period and can be very accurately represented using hourly data, as has long been recognized [e.g., Brooks, 1921]. We argue, from scientific, technological, and historical perspectives, that it is time to compute the true monthly mean using hourly data for the national and international climate data record
A three-lead, programmable, and microcontroller-based electrocardiogram generator with frequency domain characteristics of heart rate variability
Authors: Wei Ying-Chieh , Wei Ying-Yu , Chang Kai-Hsiung , Young Ming-Shing
Published: April 2012

The objective of this study is to design and develop a programmable electrocardiogram (ECG) generator with frequency domain characteristics of heart rate variability (HRV) which can be used to test the efficiency of ECG algorithms and to calibrate and maintain ECG equipment. We simplified and modified the three coupled ordinary differential equations in McSharry's model to a single differential equation to obtain the ECG signal. This system not only allows the signal amplitude, heart rate, QRS-complex slopes, and P- and T-wave position parameters to be adjusted, but can also be used to adjust the very low frequency, low frequency, and high frequency components of HRV frequency domain characteristics. The system can be tuned to function with HRV or not. When the HRV function is on, the average heart rate can be set to a value ranging from 20 to 122 beats per minute (BPM) with an adjustable variation of 1 BPM. When the HRV function is off, the heart rate can be set to a value ranging from 20 to 139 BPM with an adjustable variation of 1 BPM. The amplitude of the ECG signal can be set from 0.0 to 330 mV at a resolution of 0.005 mV. These parameters can be adjusted either via input through a keyboard or through a graphical user interface (GUI) control panel that was developed using LABVIEW. The GUI control panel depicts a preview of the ECG signal such that the user can adjust the parameters to establish a desired ECG morphology. A complete set of parameters can be stored in the flash memory of the system via a USB 2.0 interface. Our system can generate three different types of synthetic ECG signals for testing the efficiency of an ECG algorithm or calibrating and maintaining ECG equipment.
Stability analysis of self-gravitational electrostatic drift waves for a streaming nonuniform quantum dusty magnetoplasma
Authors: Bashir M. F. , Jamil M. , Murtaza G. , Salimullah M. , Shah H. A.
Published: April 2012

Using the quantum hydrodynamic model of plasmas, the stability analysis of self-gravitational electrostatic drift waves for a streaming non-uniform quantum dusty magnetoplasma is presented. For two different frequency domains, i.e., Ω0d≪ω<Ω0i (unmagnetized dust) and ω≪Ω0d<Ω0i (magnetized dust), we simplify the general dispersion relation for self-gravitational electrostatic drift waves, which incorporates the effects of density inhomogeneity ∇n0α, streaming velocity v0α due to magnetic field inhomogeneity ∇B0, Bohm potential, and the Fermi degenerate pressure. For both frequency domains, the effect of density inhomogeneity gives rise to real oscillations while the ions streaming velocity v0i as well as the effective electron quantum velocity vFe' make these oscillations propagate perpendicular to the ambient magnetic field. This oscillatory behavior of self-gravitational drift waves increases with increase in inhomogeneities and quantum effects while it decreases with increase in the gravitational potential. However, only for the unmagnetized case, the drift waves may become unstable under appropriate conditions giving rise to Jeans instability. The modified threshold condition is also determined for instability by using the intersection method for solving the cubic equation. We note that the inhomogeneity in magnetic field (equilibrium density) through streaming velocity (diamagnetic drift velocity) suppress the Jeans instability depending upon the characteristic scale length of these inhomogeneities. On the other hand, the dust-lower-hybrid wave and the quantum mechanical effects of electrons tend to reduce the growth rate as expected. A number of special cases are also discussed.
Ab initio electronic structure calculations of solid, solution-processed metallotetrabenzoporphyrins
Authors: Shea Patrick B. , Kanicki Jerzy
Published: April 2012

An ab initio study of the electronic structures of solid metallotetrabenzoporphyrins (MTBPs) utilized in organic transistors and photovoltaics is presented. Band structures, densities of states, and orbitals are calculated for H2, Cu, Ni, and Zn core substitutions of the unit cell of solid TBP, as deposited via soluble precursors that are thermally annealed to produce polycrystalline, semiconducting thin-films. While the unit cells of the studied MTBPs are nearly isomorphous, substitution of the core atoms alters the structure of the bands around the energy bandgap and the composition of the densities of states. Cu and Ni core substitutions introduce nearly dispersionless energy bands near the valence and conduction band edges, respectively, that form acceptor or deep generation/recombination states.
Auger spectrum of a water molecule after single and double core ionization
Authors: Inhester L. , Burmeister C. F. , Groenhof G. , Grubmüller H.
Published: April 2012

The high intensity of free electron lasers opens up the possibility to perform single-shot molecule scattering experiments. However, even for small molecules, radiation damage induced by absorption of high intense x-ray radiation is not yet fully understood. One of the striking effects which occurs under intense x-ray illumination is the creation of double core ionized molecules in considerable quantity. To provide insight into this process, we have studied the dynamics of water molecules in single and double core ionized states by means of electronic transition rate calculations and ab initio molecular dynamics (MD) simulations. From the MD trajectories, photoionization and Auger transition rates were computed based on electronic continuum wavefunctions obtained by explicit integration of the coupled radial Schrödinger equations. These rates served to solve the master equations for the populations of the relevant electronic states. To account for the nuclear dynamics during the core hole lifetime, the calculated electron emission spectra for different molecular geometries were incoherently accumulated according to the obtained time-dependent populations, thus neglecting possible interference effects between different decay pathways. We find that, in contrast to the single core ionized water molecule, the nuclear dynamics for the double core ionized water molecule during the core hole lifetime leaves a clear fingerprint in the resulting electron emission spectra. The lifetime of the double core ionized water was found to be significantly shorter than half of the single core hole lifetime.
Interface recombination parameters of atomic-layer-deposited Al2O3 on crystalline silicon
Authors: Werner F. , Cosceev A. , Schmidt J.
Published: April 2012

We measure the energy-dependent interface recombination parameters at the c-Si/Al2O3 interface using the frequency-dependent conductance technique. The hole capture cross section σp = (4 ± 3) × 10−16 cm2 is energy-independent, whereas the electron capture cross section σn shows a pronounced energy dependence and decreases from (7 ± 4) × 10−15 cm2 at midgap over two orders of magnitude toward the conduction band edge Ec. The capture cross section ratio at midgap is highly asymmetric with σn/σp = 5–70. The interface state density Dit is of the order of 1 × 1011 eV−1 cm−2 at midgap. Besides the main defect, a second type of defect with a capture cross section below 10−19 cm2 is resolved near the valence band edge. Numerical calculations of the injection-dependent effective surface recombination velocity using the measured interface recombination parameters show an excellent agreement with experimental data measured using the photoconductance technique.
The INE-Beamline for actinide science at ANKA
Authors: Rothe J. , Butorin S. , Dardenne K. , Denecke M. A. , Kienzler B. , Löble M. , Metz V. , Seibert A. , Steppert M. , Vitova T. , Walther C. , Geckeis H.
Published: April 2012

Since its inauguration in 2005, the INE-Beamline for actinide research at the synchrotron source ANKA (KIT North Campus) provides dedicated instrumentation for x-ray spectroscopic characterization of actinide samples and other radioactive materials. R&D work at the beamline focuses on various aspects of nuclear waste disposal within INE's mission to provide the scientific basis for assessing long-term safety of a final nuclear waste repository. The INE-Beamline is accessible for the actinide and radiochemistry community through the ANKA proposal system and the European Union Integrated Infrastructure Initiative ACTINET-I3. Experiments with activities up to 1 × 10+6 times the European exemption limit are feasible within a safe but flexible containment concept. Measurements with monochromatic radiation are performed at photon energies varying between ∼2.1 keV (P K-edge) and ∼25 keV (Pd K-edge), including the lanthanide L-edges and the actinide M- and L3-edges up to Cf. The close proximity of the INE-Beamline to INE controlled area labs offers infrastructure unique in Europe for the spectroscopic and microscopic characterization of actinide samples. The modular beamline design enables sufficient flexibility to adapt sample environments and detection systems to many scientific questions. The well-established bulk techniques x-ray absorption fine structure (XAFS) spectroscopy in transmission and fluorescence mode have been augmented by advanced methods using a microfocused beam, including (confocal) XAFS/x-ray fluorescence detection and a combination of (micro-)XAFS and (micro-)x-ray diffraction. Additional instrumentation for high energy-resolution x-ray emission spectroscopy has been successfully developed and tested.
Gate-last TiN/HfO2 band edge effective work functions using low-temperature anneals and selective cladding to control interface composition
Authors: Hinkle C. L. , Galatage R. V. , Chapman R. A. , Vogel E. M. , Alshareef H. N. , Freeman C. , Christensen M. , Wimmer E. , Niimi H. , Li-Fatou A. , Shaw J. B. , Chambers J. J.
Published: April 2012

Silicon N-metal-oxide-semiconductor (NMOS) and P-metal-oxide-semiconductor (PMOS) band edge effective work functions and the correspondingly low threshold voltages (Vt) are demonstrated using standard fab materials and processes in a gate-last scheme employing low-temperature anneals and selective cladding layers. Al diffusion from the cladding to the TiN/HfO2 interface during forming gas anneal together with low O concentration in the TiN enables low NMOS Vt. The use of non-migrating W cladding along with experimentally detected N-induced dipoles, produced by increased oxygen in the TiN, facilitates low PMOS Vt.
Theory of binless multi-state free energy estimation with applications to protein-ligand binding
Authors: Tan Zhiqiang , Gallicchio Emilio , Lapelosa Mauro , Levy Ronald M.
Published: April 2012

The weighted histogram analysis method (WHAM) is routinely used for computing free energies and expectations from multiple ensembles. Existing derivations of WHAM require observations to be discretized into a finite number of bins. Yet, WHAM formulas seem to hold even if the bin sizes are made arbitrarily small. The purpose of this article is to demonstrate both the validity and value of the multi-state Bennet acceptance ratio (MBAR) method seen as a binless extension of WHAM. We discuss two statistical arguments to derive the MBAR equations, in parallel to the self-consistency and maximum likelihood derivations already known for WHAM. We show that the binless method, like WHAM, can be used not only to estimate free energies and equilibrium expectations, but also to estimate equilibrium distributions. We also provide a number of useful results from the statistical literature, including the determination of MBAR estimators by minimization of a convex function. This leads to an approach to the computation of MBAR free energies by optimization algorithms, which can be more effective than existing algorithms. The advantages of MBAR are illustrated numerically for the calculation of absolute protein-ligand binding free energies by alchemical transformations with and without soft-core potentials. We show that binless statistical analysis can accurately treat sparsely distributed interaction energy samples as obtained from unmodified interaction potentials that cannot be properly analyzed using standard binning methods. This suggests that binless multi-state analysis of binding free energy simulations with unmodified potentials offers a straightforward alternative to the use of soft-core potentials for these alchemical transformations.
Ultrafast excited state dynamics and dispersion studies of nonlinear optical properties in dinaphthoporphycenes
Authors: Swain Debasis , Anusha P. T. , Shuvan Prashant T. , Tewari Surya P. , Sarma Tridib , Panda Pradeepta K. , Venugopal Rao S.
Published: April 2012

Ultrafast excited state dynamics of dinaphthoporphycenes were investigated using femtosecond and picosecond degenerate pump-probe techniques at 600 nm and 800 nm, respectively. Femtosecond pump-probe data indicated photo-induced absorption at 600 nm resulting from two-photon/single photon excitation, whereas picosecond pump-probe data demonstrated photo-bleaching which was a consequence of three-photon absorption. The fastest lifetimes (100–120 fs) observed are attributed to the intramolecular vibrational relaxation, the slower ones (1–3 ps) to internal conversion, and the slowest components (7–10 ps) to non-radiative decay back to ground state. Z-scan studies in the 560–600 nm range were also carried out.
Model of an impulsive subsonic jet actuator for flow control applications
Authors: Braud Caroline , Dyment Arthur
Published: April 2012

In the present contribution a physical model of the flow occurring inside impulsive actuators is developed. An impulsive actuator is characterized by its sudden flow output. The subsonic actuator under consideration is composed of a high pressure air supply and a sonic orifice driven by a valve and followed by a tube. A theoretical analysis is put forward and assessed using experimental data. It is demonstrated that the operation of such actuators essentially depends on a single parameter consisting of the reservoir to ambient pressure ratio and the throat to tube area ratio. The relationship between this parameter and others, such as the length to diameter ratio of the tube are explored. In the unsteady mode the flow inside the tube is thoroughly analyzed with the help of measurements at the exit of the tube. In addition, the time scales involved are accurately extracted, which is a crucial factor in designing closed-loop control approaches. The results obtained therefore provide an important design tool for engineering problems in flow control. Results are also applicable in the more general context of fluidic networks containing a sonic nozzle.
Smooth magnetic cusp profile calculation for axis-encircling electron beam generation
Authors: Yin Y. , Wang B. , Li H. L. , Meng L.
Published: April 2012

The calculation method of a smooth magnetic cusp profile has been introduced to obtain an axis-encircling electron beam in a fixed electrostatic field distribution. Using the calculated smooth magnetic cusp profile, an axis-encircling electron beam of current 1 A and voltage 30 kV can be obtained with a velocity ratio 1.8 and low beam ripples. Theoretical calculation and 3D simulations agree well, which show that this method can be widely used in other axis-encircling electron gun designing.
GaP collector development for SiGe heterojunction bipolar transistor performance increase: A heterostructure growth study
Authors: Skibitzki O. , Hatami F. , Yamamoto Y. , Zaumseil P. , Trampert A. , Schubert M. A. , Tillack B. , Masselink W. T. , Schroeder T.
Published: April 2012

To develop a III/V wide bandgap collector concept for future SiGe heterobipolar transistor performance increase, a heterostructure growth study of GaP on pseudomorphic 4° off-oriented Si0.8Ge0.2/Si(001) substrates was performed. For pseudomorphic GaP/Si0.8Ge0.2/Si(001) heterostructure growth, critical thickness of GaP on Si and maximum thermal budget for GaP deposition were evaluated. A detailed structure and defect characterization study by x-ray diffraction, atomic force microscopy, and transmission electron microscopy is reported on single crystalline 170 nm GaP/20 nm Si0.8Ge0.2/Si(001). Results show that 20 nm Si0.8Ge0.2/Si(001) can be overgrown by 170 nm GaP without affecting the pseudomorphism of the Si0.8Ge0.2/Si(001) layer. The GaP layer grows however partially relaxed, mainly due to defect nucleation at the GaP/Si0.8Ge0.2 interface during initial island coalescence. The achievement of 2D GaP growth conditions on Si0.8Ge0.2/Si(001) systems is thus a crucial step for achieving fully pseudomorphic heterostructures. Anti-phase domain-free GaP growth is observed for film thicknesses beyond 70 nm.
Spectrum of position fluctuations of a Brownian particle bound in a harmonic trap near a plane wall
Authors: Felderhof B. U.
Published: April 2012

The spectrum of position fluctuations of a Brownian particle bound in a harmonic trap near a plane wall is calculated from an approximate result for the Fourier transform of the velocity autocorrelation function. Both a no-slip and a perfect slip boundary condition at the wall are considered. In both cases at low frequency the calculated spectrum differs markedly from recent experimental data. It is suggested that a partial slip boundary condition with a frequency-dependent slip coefficient may explain the experimental results.
Low power sessile droplets actuation via modulated surface acoustic waves
Authors: Baudoin Michael , Brunet Philippe , Bou Matar Olivier , Herth Etienne
Published: April 2012

Low power actuation of sessile droplets is of primary interest for portable or hybrid lab-on-a-chip and harmless manipulation of biofluids. In this paper, we show that the acoustic power required to move or deform droplets via surface acoustic waves can be substantially reduced through the forcing of the drops inertio-capillary modes of vibrations. Indeed, harmonic, superharmonic, and subharmonic (parametric) excitation of these modes are observed when the high frequency acoustic signal (19.5 MHz) is modulated around Rayleigh-Lamb inertio-capillary frequencies. This resonant behavior results in larger oscillations and quicker motion of the drops than in the non-modulated case.
Modification of the surface-state occupancy on noble metal films with stacking fault arrays
Authors: Mishra Puneet , Uchihashi Takashi , Nakayama Tomonobu
Published: April 2012

Low-temperature scanning tunneling spectroscopy reveals that striped Au films grown on Ag templates containing periodic arrays of stacking faults exhibit partially populated one-dimensional (1D) surface states, in contrast to the depopulated 1D surface states on the Ag template. Detailed spectroscopic analysis on Au stripes shows the presence of 1D states with onset slightly below the Fermi level, while two-dimensional surface states exist at lower energies. These findings indicate that the Au stripes, owing to their occupied 1D surface states, may provide an effective means for 1D transport of charge and spin information between magnetic adsorbates.
A 30 T pulsed magnet with conical bore for synchrotron powder diffraction
Authors: Billette J. , Duc F. , Frings P. , Nardone M. , Zitouni A. , Detlefs C. , Roth T. , Crichton W. , Lorenzo J. E. , Rikken G. L. J. A.
Published: April 2012

We report on the design, construction, and operation of a horizontal field, 30 T magnet system with a conical bore optimized for synchrotron x-ray powder diffraction. The magnet offers ±31° optical access downstream of the sample, which allows to measure a sufficiently large number of Debye rings for an accurate crystal structure analysis. Combined with a 290 kJ generator, magnetic field pulses of 60 ms length were generated in the magnet, with a rise time of 4.1 ms and a repetition rate of 6 pulses/h at 30 T. The coil is mounted inside a liquid nitrogen bath. A liquid helium flow cryostat reaches into the coil and allows sample temperature between 5 and 250 K. The setup was used on the European Synchrotron Radiation Facility beamlines ID20 and ID06.
Global and local planarization of surface roughness by chemical vapor deposition of organosilicon polymer for barrier applications
Authors: Coclite Anna Maria , Gleason Karen K.
Published: April 2012

Particulates and asperities on the surface of plastic substrates limit the performance of the current protective barrier coatings for flexible electronics. By applying a smoothing layer to the substrate, prior to barrier deposition, permeation is reduced. While application of smoothing layers from the liquid-phase application and curing of acrylate monomers is well known, reports of planarization achieved by vapor deposition are quite limited. In the current work, the chemical vapor deposition (CVD) of a flexible smoothing layer, requiring no curing, is implemented in the same reactor chamber and from the same organosilicon monomer used for depositing the multilayer barrier stack. The process similarity between the smoothing and barrier layer deposition steps has the potential to lower the overall cost of the process and to improve interfacial properties, such as adhesion between the smoothing layer and the barrier stack. The current methods adapts and combines features of two well established methods for CVD of organic layers, plasma enhancement (PECVD) and the specific use of an initiator species (iCVD). The novel, initiated plasma enhanced chemical vapor deposition (iPECVD) method achieves a far greater degree of planarization of flexible organic layer than either of its predecessors. Polystyrene microspheres serve as model defects and allow the degree of planarization to be quantitatively measured. Both cross-sectional scanning electron micrographs and atomic force micrographs demonstrate that when the iPECVD organic layer is 1.8 µm thick, the degree of global planarization is 99%. A model demonstrates that the planarization is achieved as a result of the coating viscosity and the surface tension. Finally, the water vapor barrier performance of a 20-nm-thick SiOx layer is two orders of magnitude improved when it is deposited on a planarized substrate.
Implications of twinning kinetics on the frequency response in NiMnGa actuators
Authors: Faran Eilon , Shilo Doron
Published: April 2012

The explicit kinetic relation for twin wall motion in NiMnGa is used to correlate basic material properties to magneto-mechanical actuation rates in these crystals. In particular, we identify two parameters: the Peierls energy barrier and the twin wall mobility, which directly determine the dynamic response of NiMnGa actuators at frequencies above 10 Hz. Comparison between the kinetics of type I and type II twin walls reveals a correlation between the Peierls energy barrier and the commonly used twinning stress property. However, it is shown that twinning stress dictates twin wall dynamics only at very slow frequencies, typically below 1 Hz.
Room temperature deposition of alumina-doped zinc oxide on flexible substrates by direct pulsed laser recrystallization
Authors: Zhang Martin Y. , Nian Qiong , Cheng Gary J.
Published: April 2012

In this study, a method combining room temperature pulsed laser deposition (PLD) and direct pulsed laser recrystallization (DPLR) is introduced to deposit transparent conductive oxide (TCO) layer on low melting point flexible substrates. Alumina-doped zinc oxide (AZO), as one of the most promising TCO candidates, has now been widely used in solar cells. However, to achieve optimal, electrical, and optical properties of AZO on low melting point, flexible substrate is challenging. DPLR technique is a scalable, economic, and fast process to remove crystal defects and generate recrystallization at room temperature. It features selective processing by only heating up the TCO thin film and preserve the underlying substrate at low temperature. In this study, AZO thin film is pre-deposited by PLD on flexible and rigid substrates. DPLR is then introduced to achieve a uniform TCO layer on these substrates, i.e., commercialized Kapton polyimide film, micron-thick Al-foil, and sold lime glass (SLG). Both finite element analysis simulation and designed experiments are carried out to demonstrate that DPLR is promising in manufacturing high quality AZO layers without any damage to the underlying flexible substrates. The hall mobility of AZO after DPLR on Kapton and SLG reached 198 cm2/v · s and 398 cm2/v · s respectively, while the carrier concentrations are reduced to 2.68 × 1018 and 4.3 × 1019/cm−2, respectively. These characteristics are exactly what an ideal TCO layer should carry: high conductivity and high transmission. The property changes are due to the reduction of defect density after DPLR.
Composite non-stick droplets and their actuation with electric field
Authors: Bormashenko Edward , Pogreb Roman , Balter Revital , Gendelman Oleg , Aurbach Doron
Published: April 2012

Composite non-stick droplets comprised of di-iodomethane and water, coated by a common shell built from hydrophobic particles, are reported. Activation of the composite marbles by an electric field was studied. The water drop climbed onto the di-iodomethane drop when the composite marble was exposed to the electric field. A dimensionless constant describing sensitivity of dielectric droplets to an electric field is introduced. An explanation of the observed phenomena is proposed.
First-principles study of impurities in TlBr
Authors: Du Mao-Hua
Published: April 2012

TlBr is a promising semiconductor material for room-temperature radiation detection. Material purification has been the driver for the recent improvement in the TlBr detector performance, mainly reflected by the significant increase in the carrier mobility-lifetime product. This suggests that impurities have significant impact on the carrier transport in TlBr. In this paper, first-principles calculations are used to study the properties of a number of commonly observed impurities in TlBr. The impurity-induced gap states are presented and their effects on the carrier trapping are discussed.
The language of consecutive interpreters’ notes
Authors: Abuín Gonzàlez Marta
Published: April 2012

This paper presents an empirical study of the language of the notes produced by three groups of subjects with different levels of interpreter training and experience (beginner students, advanced students and interpreters) during an experimental consecutive interpreting task from English into Spanish. The variable under study was the note-taking language — source language vs. target language. Analyses of the notational corpus involved the application of quantitative methods so as to obtain data on the language of the notes at different skill acquisition and professional stages. The results show that as the subjects’ expertise level increases, there is a shift from the use of the source language towards the use of the target language. This finding suggests that the expertise level in consecutive interpreting may be a relevant factor in the interpreter’s choice of language. Finally, some conclusions are drawn regarding interpreter training.
The quotative ‘he/she says’ in interpreted doctor–patient interaction
Authors: Van De Mieroop Dorien
Published: April 2012

This article examines the different functions of the quotative ‘he/she says’ in an interpreter’s renderings during four medical interviews (Dutch/Russian). First, the quotative is typically used for renderings of doctors’ turns, where it serves to signal a switch in the participation framework and to segment long discourse units by the doctor. Second, in some renderings of the patients’ turns, the quotative also has a disambiguating function, clarifying the status of the interpretation either as a literal one or as an addition to a previous summary translation. Finally, in both types of interpretation the quotative also has a distancing function. However, the situations in which this function occurs vary: in the case of doctors’ turns, distancing occurs when face-threatening or dispreferred information is being given, while in the case of patients’ turns, it serves to co-construct the typical asymmetrical doctor–patient relation.
Timing of Yellow Perch Otolith Annulus Formation and Relationship between Fish and Otolith Lengths
Authors: Blackwell Brian G. , Kaufman Todd M.
Published: April 2012

We estimated the timing of annulus formation and the relationship between otolith radius length (whole view) and total length (TL) in yellow perch Perca flavescens from South Dakota lakes. Marginal increment analysis indicated that a single opaque band is formed during the summer months and that the timing of annulus formation varies with fish age. The lowest marginal increment measurements (i.e., those suggesting that annulus formation was recently completed) were most likely to occur in July, but at Waubay Lake the lowest increment for some cohorts was observed in August. Fish of age 4 or less were more likely to complete annulus formation during June. Personnel responsible for aging otoliths need to be aware of the differential timing of annulus formation. Significant relationships were observed between yellow perch TL and otolith radius length for 49 populations. Nearly all (98%) of the regression intercepts were negative. Back-calculated TLs were estimated from otolith annulus measurements using the direct proportion method and compared with the TLs previously measured for three populations. The back-calculated TL estimates were similar to the previously observed TLs, suggesting that the direct proportion method can be used to back-calculate TLs from yellow perch otoliths.

Received February 18, 2011; acceptdate November 30, 2011
Fast protein binding site comparisons using visual words representation
Authors: Pang Bin , Zhao Nan , Korkin Dmitry , Shyu Chi-Ren
Published: April 2012

Motivation: Finding geometrically similar protein binding sites is crucial for understanding protein functions and can provide valuable information for protein–protein docking and drug discovery. As the number of known protein–protein interaction structures has dramatically increased, a high-throughput and accurate protein binding site comparison method is essential. Traditional alignment-based methods can provide accurate correspondence between the binding sites but are computationally expensive.

Results: In this article, we present a novel method for the comparisons of protein binding sites using a ‘visual words’ representation (PBSword). We first extract geometric features of binding site surfaces and build a vocabulary of visual words by clustering a large set of feature descriptors. We then describe a binding site surface with a high-dimensional vector that encodes the frequency of visual words, enhanced by the spatial relationships among them. Finally, we measure the similarity of binding sites by utilizing metric space operations, which provide speedy comparisons between protein binding sites. Our experimental results show that PBSword achieves a comparable classification accuracy to an alignment-based method and improves accuracy of a feature-based method by 36% on a non-redundant dataset. PBSword also exhibits a significant efficiency improvement over an alignment-based method.

Availability: PBSword is available at http://proteindbs.rnet.missouri.edu/pbsword/pbsword.html

Contact:  shyuc@missouri.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Detection of differentially expressed segments in tiling array data
Authors: Otto Christian , Reiche Kristin , Hackermüller Jörg
Published: April 2012

Motivation: Tiling arrays have been a mainstay of unbiased genome-wide transcriptomics over the last decade. Currently available approaches to identify expressed or differentially expressed segments in tiling array data are limited in the recovery of the underlying gene structures and require several parameters that are intensity-related or partly dataset-specific.

Results: We have developed TileShuffle, a statistical approach that identifies transcribed and differentially expressed segments as significant differences from the background distribution while considering sequence-specific affinity biases and cross-hybridization. It avoids dataset-specific parameters in order to provide better comparability of different tiling array datasets, based on different technologies or array designs. TileShuffle detects highly and differentially expressed segments in biological data with significantly lower false discovery rates under equal sensitivities than commonly used methods. Also, it is clearly superior in the recovery of exon–intron structures. It further provides window z-scores as a normalized and robust measure for visual inspection.

Availability: The R package including documentation and examples is freely available at http://www.bioinf.uni-leipzig.de/Software/TileShuffle/

Contact:  joerg.hackermueller@ufz.de

Supplementary information:  Supplementary data are available at Bioinformatics online.
Approximate probabilistic analysis of biopathway dynamics
Authors: Liu Bing , Hagiescu Andrei , Palaniappan Sucheendra K. , Chattopadhyay Bipasa , Cui Zheng , Wong Weng-Fai , Thiagarajan P. S.
Published: April 2012

Motivation: Biopathways are often modeled as systems of ordinary differential equations (ODEs). Such systems will usually have many unknown parameters and hence will be difficult to calibrate. Since the data available for calibration will have limited precision, an approximate representation of the ODEs dynamics should suffice. One must, however, be able to efficiently construct such approximations for large models and perform model calibration and subsequent analysis.

Results: We present a graphical processing unit (GPU) based scheme by which a system of ODEs is approximated as a dynamic Bayesian network (DBN). We then construct a model checking procedure for DBNs based on a simple probabilistic linear time temporal logic. The GPU implementation considerably extends the reach of our previous PC-cluster-based implementation (Liu et al., 2011b). Further, the key components of our algorithm can serve as the GPU kernel for other Monte Carlo simulations-based analysis of biopathway dynamics. Similarly, our model checking framework is a generic one and can be applied in other systems biology settings.

We have tested our methods on three ODE models of bio-pathways: the epidermal growth factor–nerve growth factor pathway, the segmentation clock network and the MLC-phosphorylation pathway models. The GPU implementation shows significant gains in performance and scalability whereas the model checking framework turns out to be convenient and efficient for specifying and verifying interesting pathways properties.

Availability: The source code is freely available at http://www.comp.nus.edu.sg/~rpsysbio/pada-gpu/

Contact:  thiagu@comp.nus.edu.sg

Supplementary information:  Supplementary data are available at Bioinformatics online.
A comprehensive computational model of facilitated diffusion in prokaryotes
Authors: Zabet Nicolae Radu , Adryan Boris
Published: April 2012

Motivation: Gene activity is mediated by site-specific transcription factors (TFs). Their binding to defined regions in the genome determines the rate at which their target genes are transcribed.

Results: We present a comprehensive computational model of the search process of TF for their genomic target site(s). The computational model considers: the DNA sequence, various TF species and the interaction of the individual molecules with the DNA or between themselves. We also demonstrate a systematic approach how to parametrize the system using available experimental data.

Contact:  n.r.zabet@gen.cam.ac.uk

Supplementary information:  Supplementary data are available at Bioinformatics online.
Oocyte development and maturity classification of boarfish (Capros aper) in the Northeast Atlantic
Authors: Farrell Edward D. , Hüssy Karin , Coad Julie O. , Clausen Lotte W. , Clarke Maurice W.
Published: April 2012

Farrell, E. D., Hüssy, K., Coad, J. O., Clausen, L. W., and Clarke, M. W. 2012. Oocyte development and maturity classification of boarfish (Capros aper) in the Northeast Atlantic. – ICES Journal of Marine Science, 69: 498–507. This study presents the first detailed investigation of the oocyte development and maturity classification of boarfish, Capros aper, which has recently become the target of an industrial fishery in the Northeast Atlantic. A total of 2014 boarfish were collected from January to December 2010. Mature male and female boarfish were sexually dimorphic and could be readily identified based on external characteristics. A comprehensive maturity scale was developed, which indicated that the length at 50% maturity for males and females was 9.7 cm total length. Female boarfish were observed to spawn in Irish waters in June and July. Once spawning ceased the remaining mature oocytes were resorbed. Preliminary analysis of reproductive strategy indicates that the boarfish is likely an asynchronous batch spawner with indeterminate fecundity.