Post-detection analysis for grating-based ultra-small angle X-ray scattering.

Until recently, the hard X-ray, phase-sensitive imaging technique called grating interferometry was thought to provide information only in real space. However, by utilizing an alternative approach to data analysis we demonstrated that the angular resolved ultra-small angle X-ray scattering distribution can be retrieved from experimental data. Thus, reciprocal space information is accessible by grating interferometry in addition to real space. Naturally, the quality of the retrieved data strongly depends on the performance of the employed analysis procedure, which involves deconvolution of periodic and noisy data in this context. The aim of this article is to compare several deconvolution algorithms to retrieve the ultra-small angle X-ray scattering distribution in grating interferometry. We quantitatively compare the performance of three deconvolution procedures (i.e., Wiener, iterative Wiener and Lucy-Richardson) in case of realistically modeled, noisy and periodic input data. The simulations showed that the algorithm of Lucy-Richardson is the more reliable and more efficient as a function of the characteristics of the signals in the given context. The availability of a reliable data analysis procedure is essential for future developments in grating interferometry.

Elevated serum uric acid is associated with high circulating inflammatory cytokines in the population-based Colaus study.

BACKGROUND: The relation of serum uric acid (SUA) with systemic inflammation has been little explored in humans and results have been inconsistent. We analyzed the association between SUA and circulating levels of interleukin-6 (IL-6), interleukin-1beta (IL-1beta), tumor necrosis factor- alpha (TNF-alpha) and C-reactive protein (CRP). METHODS AND FINDINGS: This cross-sectional population-based study conducted in Lausanne, Switzerland, included 6085 participants aged 35 to 75 years. SUA was measured using uricase-PAP method. Plasma TNF-alpha, IL-1beta and IL-6 were measured by a multiplexed particle-based flow cytometric assay and hs-CRP by an immunometric assay. The median levels of SUA, IL-6, TNF-alpha, CRP and IL-1beta were 355 micromol/L, 1.46 pg/mL, 3.04 pg/mL, 1.2 mg/L and 0.34 pg/mL in men and 262 micromol/L, 1.21 pg/mL, 2.74 pg/mL, 1.3 mg/L and 0.45 pg/mL in women, respectively. SUA correlated positively with IL-6, TNF-alpha and CRP and negatively with IL-1beta (Spearman r: 0.04, 0.07, 0.20 and 0.05 in men, and 0.09, 0.13, 0.30 and 0.07 in women, respectively, P<0.05). In multivariable analyses, SUA was associated positively with CRP (beta coefficient +/- SE = 0.35+/-0.02, P<0.001), TNF-alpha (0.08+/-0.02, P<0.001) and IL-6 (0.10+/-0.03, P<0.001), and negatively with IL-1beta (-0.07+/-0.03, P = 0.027). Upon further adjustment for body mass index, these associations were substantially attenuated. CONCLUSIONS: SUA was associated positively with IL-6, CRP and TNF-alpha and negatively with IL-1beta, particularly in women. These results suggest that uric acid contributes to systemic inflammation in humans and are in line with experimental data showing that uric acid triggers sterile inflammation.

DNA-DNA interactions in bacteriophage capsids are responsible for the observed DNA knotting.

Recent experiments showed that the linear double-stranded DNA in bacteriophage capsids is both highly knotted and neatly structured. What is the physical basis of this organization? Here we show evidence from stochastic simulation techniques that suggests that a key element is the tendency of contacting DNA strands to order, as in cholesteric liquid crystals. This interaction favors their preferential juxtaposition at a small twist angle, thus promoting an approximately nematic (and apolar) local order. The ordering effect dramatically impacts the geometry and topology of DNA inside phages. Accounting for this local potential allows us to reproduce the main experimental data on DNA organization in phages, including the cryo-EM observations and detailed features of the spectrum of DNA knots formed inside viral capsids. The DNA knots we observe are strongly delocalized and, intriguingly, this is shown not to interfere with genome ejection out of the phage.

Note on the blocking flow shop problem

We present some results attained with different algorithms for the Fm|block|Cmax problem using as experimental data the well-known Taillard instances.

Kinetics of K release from soils of Brazilian coffee regions: effect of organic acids

Kinetic studies on soil potassium release can contribute to a better understanding of K availability to plants. This study was conducted to evaluate K release rates from the whole soil, clay, silt, and sand fractions of B-horizon samples of a basalt-derived Oxisol and a sienite-derived Ultisol, both representative soils from coffee regions of Minas Gerais State, Brazil. Potassium was extracted from each fraction after eight different shaking time periods (0-665 h) with either 0.001 mol L-1 citrate or oxalate at a 1:10 solid:solution ratio. First-order, Elovich, zero-order, and parabolic diffusion equations were used to parameterize the time dependence of K release. For the Oxisol, the first-order equation fitted best to the experimental data of K release, with similar rates for all fractions and independent of the presence of citrate or oxalate in the extractant solution. For all studied Ultisol fractions, in which K release rates increased when extractions were performed with citrate solution, the Elovich model described K release kinetics most adequately. The highest potassium release rate of the Ultisol silt fraction was probably due to the transference of "non-exchangeable" K to the extractant solution, whereas in the Oxisol exchangeable potassium represented the main K source in all studied fractions.

Improved multiexponential transient spectroscopy by iterative deconvolution

The analysis of multiexponential decays is challenging because of their complex nature. When analyzing these signals, not only the parameters, but also the orders of the models, have to be estimated. We present an improved spectroscopic technique specially suited for this purpose. The proposed algorithm combines an iterative linear filter with an iterative deconvolution method. A thorough analysis of the noise effect is presented. The performance is tested with synthetic and experimental data.

Microstructure and secondary phases in coevaporated CuInS2 films: Dependence on growth temperature and chemical composition

The microstructure of CuInS2-(CIS2) polycrystalline films deposited onto Mo-coated glass has been analyzed by Raman scattering, Auger electron spectroscopy (AES), transmission electron microscopy, and x-ray diffraction techniques. Samples were obtained by a coevaporation procedure that allows different Cu-to-In composition ratios (from Cu-rich to Cu-poor films). Films were grown at different temperatures between 370 and 520-°C. The combination of micro-Raman and AES techniques onto Ar+-sputtered samples has allowed us to identify the main secondary phases from Cu-poor films such as CuIn5S8 (at the central region of the layer) and MoS2 (at the CIS2/Mo interface). For Cu-rich films, secondary phases are CuS at the surface of as-grown layers and MoS2 at the CIS2/Mo interface. The lower intensity of the MoS2 modes from the Raman spectra measured at these samples suggests excess Cu to inhibit MoS2 interface formation. Decreasing the temperature of deposition to 420-°C leads to an inhibition in observing these secondary phases. This inhibition is also accompanied by a significant broadening and blueshift of the main A1 Raman mode from CIS2, as well as by an increase in the contribution of an additional mode at about 305 cm-1. The experimental data suggest that these effects are related to a decrease in structural quality of the CIS2 films obtained under low-temperature deposition conditions, which are likely connected to the inhibition in the measured spectra of secondary-phase vibrational modes.

Energy transfer mechanism and Auger effect in Er3+ coupled silicon nanoparticle samples

We report a spectroscopic study about the energy transfer mechanism among silicon nanoparticles (Si-np), both amorphous and crystalline, and Er ions in a silicon dioxide matrix. From infrared spectroscopic analysis, we have determined that the physics of the transfer mechanism does not depend on the Si-np nature, finding a fast (< 200 ns) energy transfer in both cases, while the amorphous nanoclusters reveal a larger transfer efficiency than the nanocrystals. Moreover, the detailed spectroscopic results in the visible range here reported are essential to understand the physics behind the sensitization effect, whose knowledge assumes a crucial role to enhance the transfer rate and possibly employing the material in optical amplifier devices. Joining the experimental data, performed with pulsed and continuous-wave excitation, we develop a model in which the internal intraband recombination within Si-np is competitive with the transfer process via an Auger electron"recycling" effect. Posing a different light on some detrimental mechanism such as Auger processes, our findings clearly recast the role of Si-np in the sensitization scheme, where they are able to excite very efficiently ions in close proximity to their surface. (C) 2010 American Institute of Physics.

Rpe65 microarrays, from genes to phosphorylated proteins

Purpose:To describe a novel in silico method to gather and analyze data from high-throughput heterogeneous experimental procedures, i.e. gene and protein expression arrays. Methods:Each microarray is assigned to a database which handles common data (names, symbols, antibody codes, probe IDs, etc.). Links between informations are automatically generated from knowledge obtained in freely accessible databases (NCBI, Swissprot, etc). Requests can be made from any point of entry and the displayed result is fully customizable. Results:The initial database has been loaded with two sets of data: a first set of data originating from an Affymetrix-based retinal profiling performed in an RPE65 knock-out mouse model of Leber's congenital amaurosis. A second set of data generated from a Kinexus microarray experiment done on the retinas from the same mouse model has been added. Queries display wild type versus knock out expressions at several time points for both genes and proteins. Conclusions:This freely accessible database allows for easy consultation of data and facilitates data mining by integrating experimental data and biological pathways.

Static dipole polarizability of alkali-metal clusters: Electronic exchange and correlation effects

Nonlocal approximations for the electronic exchange and correlation effects are used to compute, within density-functional theory, the polarizability and surface-plasma frequencies of small jelliumlike alkali-metal clusters. The results are compared with those obtained using the local-density approximation and with available experimental data, showing the relevance of these effects in obtaining an accurate description of the surface response of metallic clusters.

Relaxation times of non-Markovian processes

We consider a general class of non-Markovian processes defined by stochastic differential equations with Ornstein-Uhlenbeck noise. We present a general formalism to evaluate relaxation times associated with correlation functions in the steady state. This formalism is a generalization of a previous approach for Markovian processes. The theoretical results are shown to be in satisfactory agreement both with experimental data for a cubic bistable system and also with a computer simulation of the Stratonovich model. We comment on the dynamical role of the non-Markovianicity in different situations.

Thermal nucleation and cavitation in 3He and 4He

Density functionals that reproduce the helium liquid-gas interface as a function of temperature have been used, within an improved homogeneous nucleation approach, to investigate thermal nucleation and cavitation in both helium isotopes. The results are compared with available experimental data on cavitation in 3He and 4He. Predictions are made for cavitation in 3He at negative pressures and for nucleation in both isotopes.

Multipole surface-plasmon modes on simple metals

The average multipole surface-plasmon energy for simple metals, as well as that of ordinary surface and bulk plasmons, is obtained using energy-weighted moments of the electronic response to sufficiently general external perturbations. A local approximation of exchange and correlation effects is used within a jellium model. Band-structure effects are incorporated through an effective electronic mass. Taking advantage of the transparency of the method, we analyze under what circumstances such modes might be observable. It is shown that due to an interplay between Coulomb and kinetic energies, the multipole modes become unobservable for increasing values of the transferred momentum (q) parallel to the surface. The value of q at which the multipole mode becomes unobservable is much smaller than the cutoff value for Landau damping. The effect of the electronic surface diffuseness is also analyzed. We compare our results with previous density-functional calculations and with recent experimental data for Na, K, and Cs.

High-pressure ultrasonic study of vibrational anharmonicity in bcc Cu-Al-Be alloys

To quantify the vibrational anharmonicity of the long-wavelength acoustic modes of bcc Cu74.1Al23.1Be2.8 near its martensitic transition temperature Ms (261 K), the hydrostatic pressure derivatives (¿CIJ/¿P)P=0 of the elastic stiffness moduli have been measured. The Grüneisen parameters at 268 K (just above Ms), especially of longitudinal modes, which become smaller than those of the shear modes, are quite different from those at 295 K: the anharmonicity changes markedly in the vicinity of the transition. Similar trends are noted for Cu66.5Al12.7Zn20.8. Experimental data near Ms are used to estimate cubic invariants in the strain order parameters in a Landau formalism.

Vibrational behaviour of bcc Cu-based shape memory alloys close to the martensitic transition

Experimental data from ultrasonic and inelastic neutron scattering measurements are analyzed for different families of Cu-based shape-memory alloys. It is shown that the transition occurs at a value, independent of composition and alloy family, of the ratio between the elastic constants associated with the two shears necessary to accomplish the lattice distortion from the bcc to the close-packed structure. The zone boundary frequency of the TA2[110] branch evaluated at the transition point (TM), weakly depends, for each family, on composition. A linear relationship between this frequency and the inverse of the elastic constant C', both quantities evaluated at TM, has been found, in agreement with the prediction of a Landau model proposed for martensitic transformations.