A multiscale simulation system for the prediction of drug-induced cardiotoxicity

The preclinical assessment of drug-induced ventricular arrhythmia, a major concern for regulators, is typically based on experimental or computational models focused on the potassium channel hERG (human ether-a-go-go-related gene, K(v)11.1). Even if the role of this ion channel in the ventricular repolarization is of critical importance, the complexity of the events involved make the cardiac safety assessment based only on hERG has a high risk of producing either false positive or negative results. We introduce a multiscale simulation system aiming to produce a better cardiotoxicity assessment. At the molecular scale, the proposed system uses a combination of docking simulations on two potassium channels, hERG and KCNQ1, plus three-dimensional quantitative structure-activity relationship modeling for predicting how the tested compound will block the potassium currents IK(r) and IK(s). The obtained results have been introduced in electrophysiological models of the cardiomyocytes and the ventricular tissue, allowing the direct prediction of the drug effects on electrocardiogram simulations. The usefulness of the whole method is illustrated by predicting the cardiotoxic effect of several compounds, including some examples in which classic hERG-based models produce false positive or negative results, yielding correct predictions for all of them. These results can be considered a proof of concept, suggesting that multiscale prediction systems can be suitable for being used for preliminary screening in lead discovery, before the compound is physically available, or in early preclinical development when they can be fed with experimentally obtained data.     

Application of ATR-far-infrared spectroscopy to the analysis of natural resins

This study proposes FTIR spectroscopy in the far-infrared region (FarIR) as an alternative method for the characterisation of natural resins. To this purpose, standards of natural resins belonging to four different categories (sesquiterpenic, i.e. elemi, shellac; diterpenic, i.e. colophony, Venice turpentine; diterpenic with polymerised components, i.e. copal, sandarac; triterpenic, i.e. mastic and dammar) used as paint varnishes have been analysed by FarIR spectroscopy in ATR mode. Discrimination between spectral data and repeatability of measurements have been magnified and verified using principal component analysis, in order to verify the effectiveness of the method in distinguishing the four resin categories. The same samples were analysed in the MidIR range, but the spectral differences between the different categories were not evident. Moreover, the method has been tested on historical samples from the painting “La Battaglia di Cialdiran” (sixteenth century) and from a gilded leather (seventeenth century). In the first case, FarIR spectroscopy allowed confirmation of the results obtained by analytical pyrolysis. In the latter, FarIR spectroscopy proved successfully, effective in the identification of the superficial resin layer that could not be detected with the bulk chromatographic analyses.     

Reynolds Number Effects on the Coherent Dynamics of the Turbulent Horseshoe Vortex System

The adverse pressure gradient induced by a surface-mounted obstacle in a turbulent boundary layer causes the approaching flow to separate and form a dynamically rich horseshoe vortex system (HSV) in the junction of the obstacle with the wall. The Reynolds number of the flow (Re) is one of the important parameters that control the rich coherent dynamics of the vortex, which are known to give rise to low-frequency, bimodal fluctuations of the velocity field (Devenport and Simpson, J Fluid Mech 210:23–55, 1990; Paik et al., Phys Fluids 19:045107, 2007). We carry out detached eddy simulations (DES) of the flow past a circular cylinder mounted on a rectangular channel for Re = 2.0 × 10⁴ and 3.9 × 10⁴ (Dargahi, Exp Fluids 8:1–12, 1989) in order to systematically investigate the effect of the Reynolds number on the HSV dynamics. The computed results are compared with each other and with previous experimental and computational results for a related junction flow at a much higher Reynolds number (Re = 1.15 × 10⁵) (Devenport and Simpson, J Fluid Mech 210:23–55, 1990; Paik et al., Phys Fluids 19:045107, 2007). The computed results reveal significant variations with Re in terms of the mean-flow quantities, turbulence statistics, and the coherent dynamics of the turbulent HSV. For Re = 2.0 × 10⁴ the HSV system consists of a large number of necklace-type vortices that are shed periodically at higher frequencies than those observed in the Re = 3.9 × 10⁴ case. For this latter case the number of large-scale vortical structures that comprise the instantaneous HSV system is reduced significantly and the flow dynamics becomes quasi-periodic. For both cases, we show that the instantaneous flowfields are dominated by eruptions of wall-generated vorticity associated with the growth of hairpin vortices that wrap around and disorganize the primary HSV system. The intensity and frequency of these eruptions, however, appears to diminish rapidly with decreasing Re. In the high Re case the HSV system consists of a single, highly energetic, large-scale necklace vortex that is aperiodically disorganized by the growth of the hairpin mode. Regardless of the Re, we find pockets in the junction region within which the histograms of velocity fluctuations are bimodal as has also been observed in several previous experimental studies.     

Surface versus volume effects in luminescent ceria nanocrystals synthesized by an oil-in-water microemulsion method

Pure and europium (Eu(3+)) doped cerium dioxide (CeO(2)) nanocrystals have been synthesized by a novel oil-in-water microemulsion reaction method under soft conditions. In-situ X-ray diffraction and RAMAN spectroscopy, high-resolution transmission electron microscopy, UV/Vis diffuse-reflectance and Fourier transform infrared spectroscopy as well as time-resolved photoluminescence spectroscopy were used to characterize the nanaocrystals. The as-synthesized powders are nanocrystalline and have a narrow size distribution centered on 3 nm and high surface area of ~250 m(2) g(-1). Only a small fraction of the europium ions substitutes for the bulk, cubic Ce(4+) sites in the europium-doped ceria nanocrystals. Upon calcination up to 1000 °C, a remarkable high surface area of ~120 m(2) g(-1) is preserved whereas an enrichment of the surface Ce(4+) relative to Ce(3+) ions and relative strong europium emission with a lifetime of ~1.8 ms and FWHM as narrow as 10 cm(-1) are measured. Under excitation into the UV and visible spectral range, the europium doped ceria nanocrystals display a variable emission spanning the orange-red wavelengths. The tunable emission is explained by the heterogeneous distribution of the europium dopants within the ceria nanocrystals coupled with the progressive diffusion of the europium ions from the surface to the inner ceria sites and the selective participation of the ceria host to the emission sensitization. Effects of the bulk-doping and impregnation with europium on the ceria host structure and optical properties are also discussed.     

Assembly of 2D ionic layers by reaction of alkali halides with the organic electrophile 7,7,8,8-tetracyano-p-quinodimethane (TCNQ)

Sublimation of alkali halides (NaCl and LiCl) onto a pre-assembled hydrogen-bonded layer of TCNQ on Au(111) resulted in the formation of 2D ionic layers via a direct charge-transfer reaction without involvement of the substrate. The presented approach allows for the fabrication of different ionic layers, decoupled from the substrate and offering new, potentially interesting properties.     

Synthesis and characterization of [PW11O39Ir(H2O)]4-: successful incorporation of Ir into polyoxometalate framework and study of the substitutional lability at the Ir(III) site

The first Keggin-type heteropolyanion, [PW(11)O(39)Ir(H(2)O)](4-) (1), was synthesized by hydrothermal reaction from two different polytungstate precursors and [IrF(6)](2-). It was isolated as (Bu(4)N)(4)[PW(11)O(39)Ir(H(2)O)] (1a), which was completely characterized by multinuclear (31)P and (183)W NMR, ESI-mass spectrometry and cyclic voltammetry. A rapid screening methodology to ascertain the intrinsic substitutional lability at the Ir site is also presented, based on ESI-MS.     

Thermotropic and optical behaviour of new PDLC systems based on a polysulfone matrix and a cyanoazomethine liquid crystal

The thermotropic and optical characterisations of a novel polymer dispersed liquid crystal (PDLC) system based on polysulfone UDEL P-1700 as polymer matrix and a low molecular weight liquid crystal compound containing a mesogenic azomethine core and a cyano-substituent were investigated. The PDLC samples were prepared by solvent-induced phase separation (SIPS) and thermally induced phase separation (TIPS) methods using various compositions in the two components. Information on the morphology and phase structure was obtained by polarising optical microscopy, differential scanning calorimetry and X-ray diffraction measurements. PDLC systems with well-defined droplets were obtained for the composite with medium content of liquid crystal compound. The optical characterisation of these materials was performed by analysing their UV–visible absorption and photoluminescence emission as a function of the liquid crystal aggregation degree.     

Nanostructured Hybrid Systems with Rhodamine 6G

We synthesized hybrid materials by sol-gel process, using: methyltriethoxysilane, tetraetylorthosilicate and vinyltriethoxysilane, in the presence of Rhodamine 6G. It was synthesized as well organic-inorganic hybrids with addition of tetraisopropyl orthotitanate and maleic anhydride UV-VIS spectra of dye show two absorption peaks at 499 nm (dimer) and 530 nm (monomer). Evaluating FTIR spectra of hybrid films, it was observed a band at 1077 cm^?1, characteristic of the asymmetric Si-O-Si stretching vibration in oligomer. Fluorescence spectra show that tetraisopropyl orthotitanate presence in the composites modifies the nature of the inorganic matrix and affects the interaction with the added dye.     

Evaluation of the Number of Binding Sites in Proteins from their Intrinsic Fluorescence: Limitations and Pitfalls

Changes in the intrinsic protein fluorescence with the additive concentration provide one of the most employed methodologies for the evaluation of the binding constant and the number of binding sites. In the last years, more than 175 studies have been published where the double logarithmic plot shown below is used toward determining the number of equivalent binding sites ( n ). Log [( F ° ?   F ) /F]  =   log K   +   n log [Q ₀ ]. However, the value of n evaluated by this procedure is unrelated to the number of equivalent binding sites; rather it represents the stoichiometry of the binding step. The confusion on the meaning of n arises upon assuming that the binding process is represented by the forward and backward elementary steps shown below, implying that binding of the n solutes takes place simultaneously, i.e. there are no intermediate species. n Q   +   P ? Q _n P. The conclusion that n is unrelated to the number of equivalent binding sites is supported by the fact that in all the systems considered (99% of them) n values are close to one and much smaller than those obtained by ultrafiltration. It is then remarkable, the profusion of publications in peer‐reviewed, specialized journals including a conceptual error that confuses Hill′s coefficient and/or the stoichiometry of the binding step with the number of independent binding sites. Here, we discuss the origin of this common misconception and provide alternative methods to determine the number of binding sites.