bluuebunny/crossref_metadata_2025 huggingface dataset:
Protein diffusion from microwells with contrasting hydrogel domains
Authors: Su Elaine J. , Jeeawoody Shaheen , Herr Amy E.
Published: April 2019

Understanding and controlling molecular transport in hydrogel materials is important for biomedical tools, including engineered tissues and drug delivery, as well as life sciences tools for single-cell analysis. Here, we scrutinize the ability of microwells—micromolded in hydrogel slabs—to compartmentalize lysate from single cells. We consider both (i) microwells that are “open” to a large fluid (i.e., liquid) reservoir and (ii) microwells that are “closed,” having been capped with either a slab of high-density polyacrylamide gel or an impermeable glass slide. We use numerical modeling to gain insight into the sensitivity of time-dependent protein concentration distributions on hydrogel partition and protein diffusion coefficients and open and closed microwell configurations. We are primarily concerned with diffusion-driven protein loss from the microwell cavity. Even for closed microwells, confocal fluorescence microscopy reports that a fluid (i.e., liquid) film forms between the hydrogel slabs (median thickness of 1.7 μm). Proteins diffuse from the microwells and into the fluid (i.e., liquid) layer, yet concentration distributions are sensitive to the lid layer partition coefficients and the protein diffusion coefficient. The application of a glass lid or a dense hydrogel retains protein in the microwell, increasing the protein solute concentration in the microwell by ∼7-fold for the first 15 s. Using triggered release of Protein G from microparticles, we validate our simulations by characterizing protein diffusion in a microwell capped with a high-density polyacrylamide gel lid (p > 0.05, Kolmogorov-Smirnov test). Here, we establish and validate a numerical model useful for understanding protein transport in and losses from a hydrogel microwell across a range of boundary conditions.
New interaction potentials for alkali and alkaline-earth aluminosilicate glasses
Authors: Sundararaman Siddharth , Huang Liping , Ispas Simona , Kob Walter
Published: April 2019

We apply a recently developed optimization scheme to obtain effective potentials for alkali and alkaline-earth aluminosilicate glasses that contain lithium, sodium, potassium, or calcium as modifiers. As input data for the optimization, we used the radial distribution functions of the liquid at high temperature generated by means of ab initio molecular dynamics simulations and density and elastic modulus of glass at room temperature from experiments. The new interaction potentials are able to reproduce reliably the structure and various mechanical and vibrational properties over a wide range of compositions for binary silicates. We have tested these potentials for various ternary systems and find that they are transferable and can be mixed, thus allowing us to reproduce and predict the structure and properties of multicomponent glasses.
Giant number fluctuations in dry active polar fluids: A shocking analogy with lightning rods
Authors: Toner John
Published: April 2019

It has been shown [H. Chaté et al., Phys. Rev. E 77, 046113 (2008) and F. Ginelli, Eur. Phys. J.: Spec. Top. 225, 2099 (2016)] that the hydrodynamic equations of dry active polar fluids (i.e., moving flocks without momentum conservation) imply giant number fluctuations. Specifically, the rms fluctuations ⟨(δN)2⟩ of the number N of active particles in a region containing a mean number of active particles ⟨N⟩ scale according to the law ⟨(δN)2⟩=K′⟨N⟩ϕ(d) with ϕ(d)=710+15d in d ≤ 4 spatial dimensions. This is much larger than the “law of large numbers” scaling ⟨(δN)2⟩=K⟨N⟩ found in most equilibrium and nonequilibrium systems. In this paper, it is demonstrated that giant number fluctuations also depend singularly on the shape of the box in which one counts the particles, vanishing in the limit of very thin and very fat boxes. These fluctuations arise not from large density fluctuations—indeed, the density fluctuations in polar ordered dry active fluids are not in general particularly large—but from long ranged spatial correlations between those fluctuations. These are shown to be closely related in two spatial dimensions to the electrostatic potential near a sharp upward pointing conducting wedge of opening angle 3π4=135° and in three dimensions to the electrostatic potential near a sharp upward pointing charged cone of opening angle 37.16°. This very precise prediction can be stringently tested by alternative box counting experiments that directly measure the direction dependence, as well as the scaling with distance, of the density-density correlation function.
Thermal transport of nanoporous gallium nitride for photonic applications
Authors: Zhou Taofei , Zhang Cheng , ElAfandy Rami , Yuan Ge , Deng Zhen , Xiong Kanglin , Chen Fang-Ming , Kuo Yen-Kuang , Xu Ke , Han Jung
Published: April 2019

Recently, nanoporous (NP) GaN has emerged as a promising photonic material in the III-N family. Due to its attractive properties, such as its large refractive index contrast and perfect lattice matching with GaN, as well as its good electrical conductivity, photonic components and devices involving NP GaN have been successfully demonstrated. However, further development of high-performance NP GaN based electrically injected devices, such as vertical-cavity surface-emitting lasers (VCSELs) and edge emitting lasers, requires efficient heat dissipation. Therefore, in this paper, we study thermal conductivity (TC) of NP GaN, especially when incorporated into a practical distributed Bragg reflector (DBR) in a VCSEL device. Through an effective medium model, we study the theoretical effect of NP GaN morphological properties over its TC. We then experimentally measure the TC of NP GaN, with different porosities and pore wall thicknesses, which shows a high agreement with the theoretical model. We also fabricate actual NP GaN DBRs and study the large tunability and interdependence among their TC (1–24 W/m K), refractive index (0.1–1.0), and electrical conductivity (100–2000 S/m) compared to other conventional DBRs. Finally, we perform a finite-element simulation of the heat dissipation within NP GaN-VCSELs, revealing their superior thermal dissipation compared to dielectric DBR based VCSELs. In this regard, this study lays the foundation for nanoscale thermal engineering of NP GaN optoelectronic and photonic devices and paves the way for their successful commercialization.
The mechanism of RNA base fraying: Molecular dynamics simulations analyzed with core-set Markov state models
Authors: Pinamonti Giovanni , Paul Fabian , Noé Frank , Rodriguez Alex , Bussi Giovanni
Published: April 2019

The process of RNA base fraying (i.e., the transient opening of the termini of a helix) is involved in many aspects of RNA dynamics. We here use molecular dynamics simulations and Markov state models to characterize the kinetics of RNA fraying and its sequence and direction dependence. In particular, we first introduce a method for determining biomolecular dynamics employing core-set Markov state models constructed using an advanced clustering technique. The method is validated on previously reported simulations. We then use the method to analyze extensive trajectories for four different RNA model duplexes. Results obtained using D. E. Shaw research and AMBER force fields are compared and discussed in detail and show a non-trivial interplay between the stability of intermediate states and the overall fraying kinetics.
Numerical simulation of air arc impinging to chamber shell with multi-physical coupling method of fluid-thermal-structure
Authors: Wang Yujie , Wang Lijun , Jia Shenli
Published: April 2019

The air arc impinging to chamber shell during interruption current process were studied by experiments and numerical simulation. Firstly, strain characteristics of chamber shell were measured by the strain gauge, and the strain changing with times were lagging behind the pressure in arc chamber. Experiment strain results 0.0035 and 0.0025 were slightly smaller than the calculation results 0.0055 and 0.0035. Furthermore, the thermal field mathematics model of chamber shell was proposed, and it was found that there was a large temperature gradient in the thickness of the chamber shell. Lastly, stresses-strains of three kinds of coupling methods, which were the fluid-structure coupling, the thermal-structure coupling and the fluid-thermal-structure coupling were compared. It was confirmed that the mechanical stress was concentrated in the middle of the side wall, while the maximum thermal stress was distributed on the vent area. Total stress and total strain were not equal to the algebraic sum of mechanical field and thermal field. The effect of different fixed supports on the thermal field was greater than the effect on the fluid field, and outer side wall fixed support had minimal displacement.
Extracting pure absorbance spectra in infrared microspectroscopy by modeling absorption bands as Fano resonances
Authors: Schofield Alex J. , Blümel Reinhold , Kohler Achim , Lukacs Rozalia , Hirschmugl Carol J.
Published: April 2019

Midinfrared absorbance spectra obtained from spatially inhomogeneous and finite samples often contain scattering effects characterized by derivative-like bands with shifted peak positions. Such features may be interpreted and accurately modeled by Fano theory when the imaginary part of the complex dielectric function is small and Lorentzian in nature—as is the case for many biological media. Furthermore, by fitting Fano line shapes to isolated absorbance bands, recovery of the peak position and pure absorption strength can be obtained with high accuracy. Additionally, for small and optically soft spherical scatterers, recovery of one or the other of constant refractive index or radius (given approximate knowledge of the other) is possible.
High-pressure laser floating zone furnace
Authors: Schmehr Julian L. , Aling Michael , Zoghlin Eli , Wilson Stephen D.
Published: April 2019

The floating zone technique is a well-established single crystal growth method in materials research, which is able to produce volumetrically large specimens with extremely high purities. However, traditional furnace designs have relied on heating from high-powered bulb sources in combination with parabolic mirrors and hence are constrained to transparent growth chambers with large solid angles of optical access. This results in a stark limitation on achievable processing gas pressures and in turn renders a range of compounds unsuitable for crystal growth by the floating zone technique, either due to excessive volatility or due to metastability. Here, we demonstrate a novel high-pressure laser-based floating zone system (HP-LFZ). The use of lasers for heating allows implementation of a high-strength metal growth chamber, permitting greatly enhanced processing pressures over conventional mirror-based designs, with the current design allowing for pressures up to 1000 bar. We demonstrate a series of example single crystal growths using this design in pressures up to 675 bar, a significant increase over processing pressures attainable in commercially available floating zone systems. The general utility of the HP-LFZ is also illustrated via growths of a range of complex oxides.
Influence of defects on the photocatalytic behavior of La3+ ions doped SrBi2Nb2O9 ferroelectric materials
Authors: Lou Qiwei , Zeng Jiangtao , Zheng Liaoying , Man Zhenyong , Wang Wenzhong , Kassiba Abdelhadi , Park Chul Hong , Politova E. D. , Li Guorong
Published: April 2019

SrBi2–xLaxNb2O9 ferroelectric powders and ceramics were synthesized by the solid state reaction method, and the effect of La3+ ions doping on the photocatalytic efficiency was investigated. For the low doping rate x (x ≤ 0.02), the leakage current decreases, while the photocurrent and the photocatalytic efficiency increase with x. This is due to the reduction of O-vacancy and the increased spontaneous polarization. For the higher doping rate x (x > 0.02), the leakage current increases with x due to the formation of donorlike LaSr+ state, while the photocurrent and the photocatalytic efficiency decrease with x due to the increased scattering rate by LaSr+, although the spontaneous polarization increases continuously with the La3+ ions doping. These effects indicate that the defects such as LaSr+ impurity states play a more important role for the carrier transport and the photocatalysis. To our best knowledge, it is the first time that the influence of defects on the photocatalytic efficiency of ferroelectric materials is elucidated, and the results of this paper shed light on the search for new ferroelectrics with high photocatalytic performance.
Fluid-solid demixing in four and five dimensional asymmetric binary hard hypersphere mixtures
Authors: Bishop Marvin , Whitlock Paula A.
Published: April 2019

Additive asymmetric binary mixtures of hard hyperspheres in four and five dimensions are investigated by Monte Carlo simulations. These investigations probe systems with diameter ratios of 0.4 and 0.5 in which the larger hyperspheres are dominant at a mole fraction of 3/4. At the lower densities, the equations of state compare well with molecular dynamics data and a variety of theoretical predictions. When the mixture enters the metastable, two-phase regime, the smaller hyperspheres exhibit unusual phenomena as the system density increases. To understand this behavior, the mean-square displacement at equilibrium from initial lattice positions, the various pair correlation functions, and occupancy numbers are calculated. In addition, the characteristics of an initially demixed system are studied.
Analyze chemisorbed organic/metal interface by combining the two sub-interfaces model and the integer charge transfer model
Authors: Du Ying-Ying , Li Wen-Jie , Chen Guang-Hua , Lin De-Qu , Wang Long-Xi , Wu Rui , Wang Jia-Ou , Qian Hai-Jie , Ibrahim Kurash , Li Hong-Nian
Published: April 2019

The electronic structure of PC61BM film on clean Ag(100) and Ag(111) surfaces has been measured with photoemission spectroscopy. The interfaces are chemisorption. It is necessary to combine the two sub-interfaces model and the integer charge transfer model for thoroughly understanding the interfacial electronic structure. The electron injection barrier can then be determined without inverse photoemission measurements, and the PC61BM/Ag(111) system is found to be ohmic contact for electron transport. The analysis method should be applicable to many other organic/metal interfaces.
Nonlinear Landau resonance between EMIC waves and cold electrons in the inner magnetosphere
Authors: Wang Bin , Li Pengyuan , Huang Jian , Zhang Bing
Published: April 2019

It has been suggested previously that electromagnetic ion cyclotron (EMIC) waves can heat cold electrons (1–10 eV) via Landau resonance, these electrons being a source of energy for stable auroral red arc emissions. To investigate the energy transfer between cold electrons and EMIC waves in the present study, test-particle simulations were conducted to examine the interaction process at the microscopic level, with a particular focus on the nonlinearity. The nonlinear Landau resonance between cold electrons and EMIC waves was found to occur easily at normal EMIC wave amplitudes. Parametric studies were also conducted to determine how the nonlinearity depends on the electron pitch angle, energy, wave frequency, normal angle, and background plasma density. The simulation results suggest that the nonlinear resonance between EMIC waves and cold electrons is universal and probably plays an important role in damping EMIC waves in the equatorial region.
High-order harmonics generation under quasi-phase matched conditions in silver, boron, and silver sulfide plasmas of different configurations
Authors: Ganeev Rashid A. , Boltaev Ganjaboy S. , Kim Vyacheslav V. , Redkin Pavel V. , Guo Chunlei
Published: April 2019

The application of advanced methods for high-order harmonics enhancement allows the formation of conditions for phase matching of the generated harmonics in different ranges of extreme ultraviolet. We demonstrate quasi-phase matching (QPM) of the high-order harmonics generated in the plasmas containing silver microparticles and atoms, and silver sulfide molecules. The groups of harmonics in the range of 30th to 40th orders at QPM conditions prevail over the lower orders of harmonics. In most cases, the lower-order harmonics disappeared from the generated spectra at QPM conditions. The 22× enhancement factor of QPM harmonics and the 3 × 10−5 conversion efficiency for a maximally enhanced harmonic were demonstrated in the case of silver microparticle-contained plasma in the 47–67 eV energy range.
Spatial damping of extraordinary-Bernstein wave
Authors: Khokhar Tajammal H. , Yoon P. H. , Murtaza G.
Published: April 2019

The spatial propagation and attenuation of an extraordinary (X) mode wave are investigated by numerically solving the dispersion relation for Maxwellian velocity distribution. The solutions are found by taking the wave vector to be complex but the wave frequency as real, which contrasts to the customary approach of taking complex wave frequency with a real wave vector for a finite number of harmonics. The present alternative approach unveils a hitherto unknown structure associated with the dispersion relation of the X mode wave. This approach is applied to such situations where the incident wave from the outside interacts with plasma, or it is absorbed at the surface. The theoretical aspect of the banded attenuation between the harmonics is discussed, which may lead to uncovering the unforeseen applications for space and laboratory plasmas.
Molecular simulations minimally restrained by experimental data
Authors: Xu Huafeng
Published: April 2019

One popular approach to incorporating experimental data into molecular simulations is to restrain the ensemble average of observables to their experimental values. Here, I derive equations for the equilibrium distributions generated by restrained ensemble simulations and the corresponding expected values of observables. My results suggest a method to restrain simulations so that they generate distributions that are minimally perturbed from the unbiased distributions while reproducing the experimental values of the observables within their measurement uncertainties.
Experimental research on species compositions of nonequilibrium air plasma based on two-color Mach-Zehnder interferometry
Authors: Sun Hao , Wu Yi , Chen Zhexin , Rong Mingzhe , Chang Haodong , Yang Fei , Niu Chunping
Published: April 2019

An experimental method for the air plasma composition based on two-color Mach–Zehnder interferometry was established. By applying two laser beams with different wavelengths, the distributions of the temperature and nonequilibrium parameter were obtained. In the arc center, the energy exchange between the electrons and heavy particles is sufficient enough to make the plasma reach the equilibrium state. In this case, by comparing the electron density and neutral particle density derived from the interferograms, the calculated species compositions of air plasma under local thermal equilibrium were validated. Additionally, the distribution of the nonequilibrium parameter indicates that departure from the equilibrium occurs at the edge of the plasma and that the nonequilibrium area gradually expands during the arc decay phase. This trend is in good agreement with the two-temperature arc simulation, indicating the validity of the two-temperature arc model in many previous works.
Main-ion intrinsic toroidal rotation across the ITG/TEM boundary in DIII-D discharges during ohmic and electron cyclotron heating
Authors: Grierson B. A. , Chrystal C. , Haskey S. R. , Wang W. X. , Rhodes T. L. , McKee G. R. , Barada K. , Yuan X. , Nave M. F. F. , Ashourvan A. , Holland C.
Published: April 2019

Direct measurements of deuterium main-ion toroidal rotation spanning the linear ohmic to saturated ohmic confinement (LOC-SOC) regime and with additional electron cyclotron heating (ECH) are presented and compared with the more commonly measured impurity (carbon) ion rotation in DIII-D. Main ions carry the bulk of the plasma toroidal momentum, and hence, the shape of the main-ion rotation is more relevant to the study of angular momentum transport in tokamaks. Both in the LOC regime and with ECH, the main-ion toroidal rotation frequency is flat across the profile from the sawtooth region to the plasma separatrix. However, the impurity rotation profile possesses a rotation gradient, with the rotation frequency being lower near the plasma edge, implying a momentum pinch or negative residual stress inferred from the impurity rotation that differs from the main-ion rotation. In the SOC regime, both the main-ion and impurity rotation profiles develop a deeply hollow feature near the midradius while maintaining the offset in the edge rotation, both implying a positive core residual stress. In the radial region where the rotation gradient changes most dramatically, turbulence measurements show that density fluctuations near the trapped electron mode (TEM) scale are higher when the rotation profile is flat and drop significantly when the plasma density is raised and the rotation profile hollows, consistent with instabilities damped by collisions. Linear initial value gyrokinetic simulations with GYRO indicate that the transition from LOC-SOC in DIII-D occurs as TEMs are replaced by ion temperature gradient (ITG) driven modes from the outer radii inwards as the plasma collisionality increases, Zeff decreases, and the power flow through the ion channel progressively increases due to the electron-ion energy exchange. Gyrofluid modeling with trap gyro-Landau fluid (TGLF) successfully reproduces the plasma profiles at key times in the discharge and in time dependent simulations with predictive TRANSP. TGLF indicates that in the LOC and SOC regimes as well as with ECH, subdominant modes are present and that the plasma is not in a pure TEM or ITG binary state, but rather a more subtle mixed state. Predictions of the main-ion rotation profiles are performed with global nonlinear gyrokinetic simulations using GTS and reveal that the flat rotation is due to oscillatory variation of the turbulent residual stress across the profile, whereas the deeply hollow rotation profile is due to a larger-scale, dipole-like stress profile. In these cases, the predicted and observed main-ion rotation profile is consistent with the balance of turbulent residual stress and momentum diffusion.
Chaotic behavior of Eulerian magnetohydrodynamic turbulence
Authors: Ho Richard D. J. G. , Berera Arjun , Clark Daniel
Published: April 2019

We study the chaotic properties of a turbulent conducting fluid using direct numerical simulation in the Eulerian frame. The maximal Lyapunov exponent is measured for simulations with varying Reynolds number and magnetic Prandtl number. We extend the Ruelle theory of hydrodynamic turbulence to magnetohydrodynamic turbulence as a working hypothesis and find broad agreement with the results. In other simulations, we introduce magnetic helicity and these simulations show a diminution of chaos, which is expected to be eliminated at the maximum helicity. We also find that the difference between two initially close fields grows linearly at late times, which was also recently found in hydrodynamics. This linear growth rate is found to be dependent on the dissipation rate of the relevant field. We discuss the important consequences this linear growth has on predictability. We infer that the chaos in the system is totally dominated by the velocity field and connect this work to real magnetic systems such as solar weather and confined plasmas.
Optimization of band-selective homonuclear dipolar recoupling in solid-state NMR by a numerical phase search
Authors: Zhang Zhengfeng , Liu Hui , Deng Jing , Tycko Robert , Yang Jun
Published: April 2019

Spin polarization transfers among aliphatic 13C nuclei, especially 13Cα–13Cβ transfers, permit correlations of their nuclear magnetic resonance (NMR) frequencies that are essential for signal assignments in multidimensional solid-state NMR of proteins. We derive and demonstrate a new radio-frequency (RF) excitation sequence for homonuclear dipolar recoupling that enhances spin polarization transfers among aliphatic 13C nuclei at moderate magic-angle spinning (MAS) frequencies. The phase-optimized recoupling sequence with five π pulses per MAS rotation period (denoted as PR5) is derived initially from systematic numerical simulations in which only the RF phases are varied. Subsequent theoretical analysis by average Hamiltonian theory explains the favorable properties of numerically optimized phase schemes. The high efficiency of spin polarization transfers in simulations is preserved in experiments, in part because the RF field amplitude in PR5 is only 2.5 times the MAS frequency so that relatively low 1H decoupling powers are required. Experiments on a microcrystalline sample of the β1 immunoglobulin binding domain of protein G demonstrate an average enhancement factor of 1.6 for 13Cα → 13Cβ polarization transfers, compared to the standard 13C–13C spin-diffusion method, implying a two-fold time saving in relevant 2D and 3D experiments.
Effects of chemical defects on anisotropic dielectric response of polyethylene
Authors: Fukushima Shogo , Tiwari Subodh , Kumazoe Hiroyuki , Kalia Rajiv K. , Nakano Aiichiro , Shimojo Fuyuki , Vashishta Priya
Published: April 2019

Dielectric polymers such as polyethylene (PE) have a wide range of energy and electronic applications. While recent studies have shown significant effects of chemical defects on the electronic structure of PE, those on the dielectric properties remain elusive. Here, first-principles quantum-mechanical calculations show anisotropic dielectric constants of PE, which are sensitive to the type of defects. Specifically, addition of iodine defects increases the high-frequency dielectric constant. Addition of hydroxyl or carboxyl group, on the other hand, causes noticeable anisotropic changes in the static dielectric constant, which is well elucidated through the rotation and concerted motions of chemical groups. The sensitivity of these defects may be exploited to rationally alter the behavior of PE.
Sample seal-and-drop device and methodology for high temperature oxide melt solution calorimetric measurements of PuO2
Authors: Guo Xiaofeng , Boukhalfa Hakim , Mitchell Jeremy N. , Ramos Michael , Gaunt Andrew J. , Migliori Albert , Roback Robert C. , Navrotsky Alexandra , Xu Hongwu
Published: April 2019

Thermodynamic properties of refractory materials, such as standard enthalpy of formation, heat content, and enthalpy of reaction, can be measured by high temperature calorimetry. In such experiments, a small sample pellet is dropped from room temperature into a calorimeter operating at high temperature (often 700 °C) with or without a molten salt solvent present in an inert crucible in the calorimeter chamber. However, for hazardous (radioactive, toxic, etc.) and/or air-sensitive (hygroscopic, sensitive to oxygen, pyrophoric, etc.) samples, it is necessary to utilize a sealed device to encapsulate and isolate the samples, crucibles, and solvent under a controlled atmosphere in order to prevent the materials from reactions and/or protect the personnel from hazardous exposure during the calorimetric experiments. We have developed a sample seal-and-drop device (calorimetric dropper) that can be readily installed onto the dropping tube of a calorimeter such as the Setaram AlexSYS Calvet-type high temperature calorimeter to fulfill two functions: (i) load hazardous or air-sensitive samples in an air-tight, sealed container and (ii) drop the samples into the calorimeter chamber using an “off-then-on” mechanism. As a case study, we used the calorimetric dropper for measurements of the enthalpy of drop solution of PuO2 in molten sodium molybdate (3Na2O·4MoO3) solvent at 700 °C. The obtained enthalpy of −52.21 ± 3.68 kJ/mol is consistent with the energetic systematics of other actinide oxides (UO2, ThO2, and NpO2). This capability has thus laid the foundation for thermodynamic studies of other Pu-bearing phases in the future.
High order harmonic radiation source for multicolor extreme ultraviolet radiography of carbon plumes
Authors: Kumar M. , Singhal H. , Chakera J. A.
Published: April 2019

Multicolor radiography is used for the characterization of atoms, ions, and molecules of carbon plasma plumes formed by focusing a 200 ps Ti:sapphire laser pulse on a solid graphite target. The radiography of the plume was carried out using a high order harmonic generation based radiation source consisting of the 11th (λ ≈ 72.7 nm) to 21st (λ ≈ 38 nm) odd harmonic orders of the Ti:sapphire laser pulse. The density profile of CI, CII, and carbon dimer molecule (C2) is estimated from the 2D-transmission profile of the harmonics, recorded after passing through the carbon plume. The peak densities of CI, CII, and C2 at a 50 ns delay are estimated to be 8 × 1024 m−3, 4 × 1024 m−3, and 3.5 × 1023 m−3 at distances of 150 μm, 170 μm, and 120 μm away from the target surface, respectively. The expansion speed of the plasma plume front is estimated to be 2 × 104 m/s and the speed of the C2 molecule to be 4 × 103 m/s at a laser intensity of 1011 W cm−2. The present study demonstrates ultrafast multicolor radiography as a simple and versatile tool for a simultaneous estimation of the density profile of neutral atoms, ions, and molecular species of the plasma plume.
New spin logic device constructed using asymmetric quantum wells
Authors: Johnson-Groh Mara
Published: April 2019

A new spin logic device that uses electrochemical potentials has been shown to be quicker and more energy efficient than traditional devices.
Proposed probe chip a potential shortcut for quantum device manufacturing cycle
Authors: Patrick Chris
Published: April 2019

Alternative method of characterizing semiconductor material properties with a separate probe chip that induces quantum dots could speed optimization of quantum dot spin qubits.
Hybrid materials based on graphene derivatives and porphyrin metal-organic frameworks
Authors: Arslanov Vladimir V. , Kalinina Maria A. , Ermakova Elizaveta V. , Raitman Oleg A. , Gorbunova Yulia G. , Aksyutin Oleg E. , Ishkov Alexander G. , Grachev Vladimir A. , Tsivadze Aslan Yu.
Published: April 2019

Domestic and foreign literature on methods for obtaining graphene and its derivatives [graphene oxide (GO) and reduced GO] as representatives of the family of 2D layered materials is analyzed. Particular attention is paid to GO. Great potential of post-synthetic modification as well as unique properties of the material and its derivatives make them promising for a variety of applications including biomedicine, ecology, optoelectronics, etc. Chemical and physical methods for the reduction of GO to obtain graphene-like materials similar in structure and properties to pure graphene obtained by direct mechanical cleavage are considered. Functionalization strategies of graphene materials are discussed. The preparation of hydro- and organogels as well as Pickering emulsions from graphene derivatives as precursors of porous monoliths are considered. The formation of aerogels based on graphene materials and methane adsorption on these porous structures are discussed. Basic information about hybrid materials containing graphene derivatives and metal-organic frameworks is given and their adsorption characteristics with respect to methane are evaluated. Covalent and noncovalent interactions in graphene – porphyrin hybrids are considered from the standpoint of formation of porphyrin architectures on the surface of graphene materials. Examples of the use of porphyrin – graphene composite materials in photo- and electrocatalysis, fuel cells and gas separation membranes are given.

The bibliography includes 243 references.
The impact of neglecting user-centered information design principles when delivering online information
Authors: Santos Lonsdale Maria dos , Lonsdale David J. , Lim Hye-Won
Published: April 2019

Information design principles are overlooked in cyber security awareness websites. An Information Design Process
Model has been devised to help frame and interpret how online information is processed and the role information design principles
play in facilitating that processing. Two websites have been compared, and results show significant differences in terms of
performance, behavior and perception. The results also show that in situations where serious information is at stake, such as
cyber security, a more accessible design does not seem to be sufficient to project a sense of trust and security among users. All
these findings have led to original insights regarding the design of online information in terms of lasting impression and
user-centered design approaches.
Vanillic acid in Panax ginseng root extract inhibits melanogenesis in B16F10 cells via inhibition of the NO/PKG signaling pathway
Authors: Liu Jianzeng , Xu Xiaohao , Jiang Rui , Sun Liwei , Zhao Daqing
Published: April 2019

Panax ginseng C. A. Meyer has been widely used in skin care. Our previous study showed that the phenolic acids in ginseng root extract (GRE) impart inhibitory effects on melanogenesis. In this study, we found that as the most abundant component of phenolic acids in GRE, vanillic acid decreased tyrosinase activity and melanin levels with or without α-MSH stimulation and suppressed the expression of microphthalmia-associated transcription factor (MITF) and melanogenic enzymes in B16F10 cells. Furthermore, vanillic acid downregulated NOS activity, nitric oxide (NO) content, cGMP level, guanylate cyclase (GC) and protein kinase G (PKG) activity, and the phosphorylation of cAMP-response element-binding protein (CREB), whereas arbutin had no effect on the NO/PKG pathway. These findings indicate that vanillic acid in GRE suppressed melanogenesis by inhibiting the NO/PKG signaling pathways. This study provides a potential mechanism underlying the inhibitory effect of ginseng on melanogenesis.
Long non-coding RNA ZFAS1 regulates the malignant progression of gastric cancer via the microRNA-200b-3p/Wnt1 axis
Authors: Zhang Fan , Li Ying , Xu Weiran , He Liang , Tan Yan , Xu Hong
Published: April 2019

Gastric cancer is a common malignant tumor. Studies from our laboratory or others have shown that long non-coding RNA (lncRNA) zinc finger antisense (ZFAS)1 often acts as an oncogene. However, the molecular underpinnings of how ZFAS1 regulates gastric cancer remain to be elucidated. Results showed that ZFAS1 expression was upregulated, and microRNA-200b-3p (miR-200b) expression was downregulated in gastric cancer tissues. MiR-200b overexpression suppressed the proliferation, cell cycle process, and Wnt/β-catenin signaling of gastric cancer cells. Subsequently, we identified miR-200b is a target of ZFAS1 and Wnt1 is a target of miR-200b. Furthermore, promotion of cancer malignant progression and activation of Wnt/β-catenin signaling induced by ZFAS1 was counteracted by increasing miR-200b expression. In vivo, ZFAS1 knockdown suppressed the tumorigenesis with the upregulated miR-200b and the inactive Wnt/β-catenin signaling. Summarily, we demonstrated a critical role of miR-200b in gastric cancer, and ZFAS1 can promote malignant progression through regulating miR-200b mediated Wnt/β-catenin signaling.
Uptake of adenine by purine permeases of Coffea canephora
Authors: Kakegawa Hirofumi , Shitan Nobukazu , Kusano Hiroaki , Ogita Shinjiro , Yazaki Kazufumi , Sugiyama Akifumi
Published: April 2019

Purine permeases (PUPs) mediate the proton-coupled uptake of nucleotide bases and their derivatives into cytosol. PUPs facilitate uptake of adenine, cytokinins and nicotine. Caffeine, a purine alkaloid derived from xanthosine, occurs in only a few eudicot species, including coffee, cacao, and tea. Although caffeine is not an endogenous metabolite in Arabidopsis and rice, AtPUP1 and OsPUP7 were suggested to transport caffeine. In this study, we identified 15 PUPs in the genome of Coffea canephora. Direct uptake measurements in yeast demonstrated that CcPUP1 and CcPUP5 facilitate adenine – but not caffeine – transport. Adenine uptake was pH-dependent, with increased activity at pH 3 and 4, and inhibited by nigericin, a potassium–proton ionophore, suggesting that CcPUP1 and CcPUP5 function as proton-symporters. Furthermore, adenine uptake was not competitively inhibited by an excess amount of caffeine, which implies that PUPs of C. canephora have evolved to become caffeine-insensitive to promote efficient uptake of adenine into cytosol.
Anti-photoaging effect of skin cream manufactured with ziyuglycoside I isolated from Sanguisorba officinalis on ultraviolet B-induced hairless mice
Authors: Yun Mi-Young , Bae Eun-Young , Lee Seung-Woong , Yim Soon-Ho , Ly Sun-Yung , Choi Hwa-Jung
Published: April 2019

In this study, skin cream containing ziyuglycoside I isolated from Sanguisorba officinalis was manufactured and examined the protective effects of the skin cream against UVB-induced hairless mice. UVB-induced hairless mice were topically treated with the skin cream once a day for 5 weeks. Application of the skin cream did not exhibit side effect on body growth showing normal body weight and food efficiency in the mice. The skin cream treatment also was inhibited mRNA expression of interleukin (IL)-1β, matrix metalloproteinase (MMP)-2, MMP-9, and MMP-2 protein expression in the mice. Furthermore, the skin cream treatment inhibits epidermal wrinkle formation, wrinkle depth, wrinkle thickness, and collagen degradation in UVB-induced hairless mice. Therefore, the skin cream was able to play a role in the attenuation of photoaging caused by UVB irradiation via downregulation of mRNA expression of inflammatory cytokine IL-1β, MMP-2, MMP-9, and suppression of MMP-2 proteins expression.
Fat Extract Improves Random Pattern Skin Flap Survival in a Rat Model
Authors: Cai Yizuo , Yu Ziyou , Yu Qian , Zheng Hongjie , Xu Yuda , Deng Mingwu , Wang Xiangsheng , Zhang Lu , Zhang Wenjie , Li Wei
Published: April 2019

Background

Adipose tissue and its derivatives, including adipose-derived stem cells, stromal vascular fraction (SVF), and SVF-gel, have been utilized in the treatment of many ischemic disorders. However, the utilization of these products is limited in clinical applications by concerns related to the presence of cells in these derivatives.

Objectives

This study aimed to isolate a cell-free fat extract (FE) from fat tissue and to evaluate its proangiogenic ability in vitro as well as its protective effects on skin flap survival in vivo.

Methods

FE was isolated from human fat via a mechanical approach. The concentrations of several growth factors in the FE were determined by enzyme-linked immunosorbent assay. The proangiogenic ability of FE was evaluated utilizing assays of the proliferation, migration, and tube formation in human umbilical vein endothelial cells in vitro. The protective effects of FE on the survival of random pattern skin flaps were investigated by subcutaneous injection into rats.

Results

Enzyme-linked immunosorbent assay results revealed that FE contained proangiogenic growth factors that promoted proliferation, migration, and tube formation in human umbilical vein endothelial cells in vitro. In addition, FE reduced skin flap necrosis and increased survival, as demonstrated by macroscopic measurements and blood flow analysis. Histological analysis revealed that FE treatment increased the capillary density.

Conclusions

FE is a cell-free, easy-to-prepare, and growth-factor–enriched liquid derived from human adipose tissue that possesses proangiogenic activity and improves skin flap survival by accelerating blood vessel formation. FE may be potentially used for treating ischemic disorders.
Systematic analysis of supervised machine learning as an effective approach to predicate β-lactam resistance phenotype in Streptococcus pneumoniae
Authors: Zhang Chaodong , Ju Yingjiao , Tang Na , Li Yun , Zhang Gang , Song Yuqin , Fang Hailing , Yang Liang , Feng Jie
Published: April 2019

Streptococcus pneumoniae is the most common human respiratory pathogen, and β-lactam antibiotics have been employed to treat infections caused by S. pneumoniae for decades. β-lactam resistance is steadily increasing in pneumococci and is mainly associated with the alteration in penicillin-binding proteins (PBPs) that reduce binding affinity of antibiotics to PBPs. However, the high variability of PBPs in clinical isolates and their mosaic gene structure hamper the predication of resistance level according to the PBP gene sequences. In this study, we developed a systematic strategy for applying supervised machine learning to predict S. pneumoniae antimicrobial susceptibility to β-lactam antibiotics. We combined published PBP sequences with minimum inhibitory concentration (MIC) values as labelled data and the sequences from NCBI database without MIC values as unlabelled data to develop an approach, using only a fragment from pbp2x (750 bp) and a fragment from pbp2b (750 bp) to predicate the cefuroxime and amoxicillin resistance. We further validated the performance of the supervised learning model by constructing mutants containing the randomly selected pbps and testing more clinical strains isolated from Chinese hospital. In addition, we established the association between resistance phenotypes and serotypes and sequence type of S. pneumoniae using our approach, which facilitate the understanding of the worldwide epidemiology of S. pneumonia.
kmcEx: memory-frugal and retrieval-efficient encoding of counted k-mers
Authors: Jiang Peng , Luo Jie , Wang Yiqi , Deng Pingji , Schmidt Bertil , Tang Xiangjun , Chen Ningjiang , Wong Limsoon , Zhao Liang
Published: April 2019

Motivation

K-mers along with their frequency have served as an elementary building block for error correction, repeat detection, multiple sequence alignment, genome assembly, etc., attracting intensive studies in k-mer counting. However, the output of k-mer counters itself is large; very often, it is too large to fit into main memory, leading to highly narrowed usability.

Results

We introduce a novel idea of encoding k-mers as well as their frequency, achieving good memory saving and retrieval efficiency. Specifically, we propose a Bloom filter-like data structure to encode counted k-mers by coupled-bit arrays—one for k-mer representation and the other for frequency encoding. Experiments on five real datasets show that the average memory-saving ratio on all 31-mers is as high as 13.81 as compared with raw input, with 7 hash functions. At the same time, the retrieval time complexity is well controlled (effectively constant), and the false-positive rate is decreased by two orders of magnitude.

Availability and implementation

The source codes of our algorithm are available at github.com/lzhLab/kmcEx.

Supplementary information

Supplementary data are available at Bioinformatics online.
Maximizing Achievable Transmission Time in Cognitive Radio Networks Under Sensor-Aided Crowdsourced Spectrum Sensing
Authors: Almasaeid Hisham M
Published: April 2019

Spectrum-sensing as a service has been proposed and studied by many researchers over the past decade as a promising approach to support the viability of cognitive radio networks (CRNs). A spectrum-sensing service provider (SSP) provides information about spectrum occupancy to its clients that is generally more accurate than what clients can learn on their own. Two approaches are used by SSPs in their operation, the dedicated sensing infrastructure approach (sensor-aided CRN) and the crowdsensing approach. In this work, we assume a hybrid model where a dedicated sensing infrastructure is used along with crowdsensing. We study the tradeoff between sensing time paid by cognitive users to the SSP and their achievable transmission time. Our objective is to maximize the minimum achievable transmission time for any cognitive user in the network by carefully selecting the channels to be used. Two algorithms are proposed, one is based on the hill-climbing search algorithm (abbreviated HCA) and the other is a less optimal but faster greedy selection algorithm (abbreviated GSA). Results show that both HCA and GSA are within 3% of the optimal solution. Results also confirm that GSA is faster than HCA, while HCA outperforms GSA.
Genomic and mitochondrial evidence of ancient isolations and extreme introgression in the four-lined snake
Authors: Thanou Evanthia , Kornilios Panagiotis , Lymberakis Petros , Leaché Adam D
Published: April 2019

Comparing mitochondrial and genomic phylogenies is an essential tool for investigating speciation processes, because each genome carries different inheritance properties and evolutionary characteristics. Furthermore, mitonuclear discordance may arise from ecological adaptation, historic isolation, population size changes, and sex-biased dispersal. Closely related taxa are expected to experience gene flow; however, this may not be true for insular populations or populations isolated in refugia. The four-lined snake Elaphe quatuorlineata has a fragmented distribution, separating populations of the Italian and Balkan Peninsulas, whereas several insular Aegean populations of significantly smaller body size (Cyclades island group and Skyros Island, Greece) are currently considered distinct subspecies. We constructed the species-tree phylogeny of this species utilizing genome-wide single nucleotide polymorphisms and a gene-tree based on complete cytochrome b sequences, aiming to detect convergence and discrepancies between biparentally and maternally inherited genomes. Population structuring, phylogenetic patterns and migration events among geographically defined lineages supported our hypothesis of isolation in multiple sub-refugia. Where biogeographical barriers did not restrict subsequent dispersal, extensive genetic exchange occurred between mainland Balkan populations. This process has led to the mitochondrial sweep of an ancestral mitolineage that survived only in peripheral (East Greece) and insular populations (North Cyclades and Skyros). The Central Cyclades represent an ancient lineage for both molecular markers that emerged almost 3.3 Mya. Considering their distinct morphology, insular E. quatuorlineata populations should be the future focus of an extensive sampling, especially since the mitonuclear discordance observed in this species could be related to ecological adaptations, such as the island-dwarfism phenomenon.
A Transatlantic Secular Divide? The Representation of Religion in EU and US Foreign Policy
Authors: Jenichen Anne
Published: April 2019

It is a common—often stereotypical—presumption that Europe is secular and America religious. Differences in international religious freedom and religious engagement policies on both sides of the Atlantic seem to confirm this “cliché.” This article argues that to understand why it has been easier for American supporters to institutionalize these policies than for advocates in the EU, it is important to consider the discursive structures of EU and US foreign policies, which enable and constrain political language and behavior. Based on the analysis of foreign policy documents, produced by the EU and the United States in their relationship with six religiously diverse African and Asian states, the article compares how both international actors represent religion in their foreign affairs. The analysis reveals similarities in the relatively low importance that they attribute to religion and major differences in how they represent the contribution of religion to creating and solving problems in other states. In sum, the foreign policies of both international actors are based on a secular discursive structure, but that of the United States is much more accommodative toward religion, including Islam, than that of the EU.