Oversampling Free Energy Perturbation Simulation in Determination of the Ligand-Binding Free Energy

Determination of the ligand-binding affinity is an extremely interesting problem. Normally, the free energy perturbation (FEP) method provides an appropriate result. However, it is of great interest to improve the accuracy and precision of this method. In this context, temperature replica exchange molecular dynamics implementation of the FEP computational approach, which we call replica exchange free energy perturbation (REP) was proposed. In particular, during REP simulations, the system can easily escape from being trapped in local minima by exchanging configurations with high temperatures, resulting in significant improvement in the accuracy and precision of protein–ligand binding affinity calculations. The distribution of the decoupling free energy was enlarged, and its mean values were decreased. This results in changes in the magnitude of the calculated binding free energies as well as in alteration in the binding mechanism. Moreover, the REP correlation coefficient with respect to experiment ( R^REP = 0.85 ± 0.15 ) is significantly boosted in comparison with the FEP one ( R^FEP = 0.64 ± 0.30 ). Furthermore, the root-mean-square error (RMSE) of REP is also smaller than FEP, RMSE^REP = 4.28 ± 0.69 versus RMSE^FEP = 5.80 ± 1.11 kcal/mol, respectively. © 2019 Wiley Periodicals, Inc.     

Mycotoxins in spices and culinary herbs from Italy and Tunisia

Abstract

Spices and aromatic herbs can be contaminated with mycotoxins, since of their preharvest, postharvest, and storage conditions. In this study, 112 samples of different spices and aromatic herbs were evaluated for their mycotoxins content by HPLC-MS/MS in order to highlight their possible risk linked with human use. The results showed that mycotoxins were occasionally detected only in samples of coriander, laurel, mint, rosemary, and verbena. In both geographical origins a different contamination was detected. Among the investigated mycotoxins, AFB2, AFG1, AFG2, T2 and HT2 were detected, whereas none of the samples contained AFB1 and FB1. The co-occurrence of two toxins were observed for some samples of rosemary and verbena. This study indicates that it is essential minimize the toxins in agriculture, industry, and food-product manufacturing for the consumer health protection.     

High-precision sub-pixel interpolation in particle image velocimetry image processing

The task of image interpolation and re-sampling for particle image velocimetry (PIV) is investigated, which is used for window shifting with sub-pixel accuracy and image or window deformation. A new interpolation scheme based on a Gaussian filter is introduced and compared with commonly used and widely accepted interpolation techniques in terms of the achievable root mean square deviation of the displacement estimates.     

Comparative study of Euler/Euler and Euler/Lagrange approaches simulating evaporation in a turbulent gas–liquid flow

This study deals with the Reynolds‐averaged Navier–Stokes simulation of evaporation in a turbulent gas–liquid flow in a three‐dimensional duct, focussing on the results obtained by a four‐equation turbulence model within the framework of the Euler/Euler approach for multiphase flow calculations: in addition to the two‐equation k?ε model describing the turbulence of the continuous (C) phase, the computational model employs transport equations for the turbulence kinetic energy of the disperse (D) phase and for the velocity covariance q=〈{u}^D{u}^C〉^D. In the present study, the evaporation model according to Abramzon and Sirignano (Int. J. Heat Mass Transfer 1989; 32 :1605–1618) has been extended by introducing an additional transport equation for a newly defined quantity ā, defined as the phase‐interface surface fraction. This allows the change in the drop diameter to be quantified in terms of a probability density function. The source term in the equation describing the dynamics of the volumetric fraction of the dispersed phase α^D is related to the evaporation time scale τ_Γ. The performance of the new model is evaluated by performing a comparative analysis of the results obtained by simulating a polydispersed spray in a three‐dimensional duct configuration with the results of the Euler/Lagrange calculations performed in parallel. Prior to these calculations, some selected (solid) particle‐laden flow configurations were computationally examined with respect to the validation of the background, four‐equation, eddy‐viscosity‐based turbulence model. Copyright © 2008 John Wiley & Sons, Ltd.     

Simultaneous PIV and concentration measurements in a gas-turbine combustor model

Simultaneous velocity and concentration measurements have been performed in a gas-turbine combustor model. Particle image velocimetry (PIV) was used to acquire planar velocity information and to identify coherent flow structures. The Mie scattering technique, based on a slightly modified experimental setup, was used for concentration measurements in this mixing flow. The degree of mixing was assessed by examining local concentration measurements while inhomogeneously seeding the primary and secondary stream of the mixing layer. Connections between flow field and concentration distribution were highlighted using the proper orthogonal decomposition algorithm (POD). Uncertainties and systematic errors for the PIV measurements due to the suboptimal seeding are discussed using a comparison with a second test series at optimal seeding conditions. Results are presented for several flow parameters and at various lateral planes.     

Ankyrin repeat and SOCS box containing protein 4 (Asb-4) colocalizes with insulin receptor substrate 4 (IRS4) in the hypothalamic neurons and mediates IRS4 degradation

Background

Cigarette smoking enhances the risk of stroke. However, the underlying molecular mechanisms are largely unknown. The present study established an in vivo rat secondhand cigarette smoking (SHS) model and examined the hypothesis that SHS upregulates endothelin receptors with increased cerebrovascular contraction via the Raf/extracellular signal-regulated kinase (ERK)/mitogen-activated protein kinases (MAPK) pathway.

Results

Rats were exposed to SHS for up to 8 weeks. The cerebral artery vasoconstriction was recorded by a sensitive myograph. The mRNA and protein expressions for endothelin receptors in cerebral arteries were studied by real-time PCR and Western blot. Compared to fresh air exposed rats, cerebral arteries from SHS rats exhibited stronger contractile responses (P < 0.05) mediated by endothelin type A (ET_A) receptors. The expressions of mRNA and protein for ET_A receptors in the cerebral arteries from SHS rats were higher (P < 0.05) than that in control. SHS did not affect endothelin type B (ET_B) receptor-mediated contractions, mRNA or protein levels. The results suggest that SHS upregulates ET_A, but not ET_B receptors in vivo. After SHS exposure, the mRNA levels of Raf-1 and ERK1/2, the protein expression of phosphorylated (p)-Raf-1 and p-ERK1/2 were increased (P < 0.05). Raf-1 inhibitor, GW5074 suppressed the enhanced ET_A receptor-mediated contraction, mRNA and protein levels induced by SHS. In addition, GW5074 inhibited the SHS-caused increased mRNA and phosphorylated protein levels of Raf-1 and ERK1/2, suggesting that SHS induces activation of the Raf/ERK/MAPK pathway.

Conclusions

SHS upregulates cerebrovascular ET_A receptors via the Raf/ERK/MAPK pathway, which provides novel understanding of mechanisms involved in SHS-associated stroke.     

Design and performance of millimeter-wave end-coupled bandpass filters

The design and performance of millimeter-wave microstrip/suspended-stripline end-coupled bandpass filters are presented. Filters in Ka-band (26.5 to 40 GHz) and W-band (75 to 110 GHz) using suspended-stripline and microstrip have been designed. Good agreement between the experimental results and those predicted theoretically was observed. Measured passband insertion losses of less than 1 and 0.5 dB have been achieved in W- and Ka-band, respectively. An extremely wideband waveguide-to-microstrip transition with an insertion loss of 0.25 dB over the full W-band is also presented.     

A statistical method for transforming temporal correlation functions from one-point measurements into longitudinal spatial and spatio-temporal correlation functions

The transformation of temporal, one-point correlation functions into longitudinal spatial and spatio-temporal correlation functions in turbulent flows using a simple statistical convection model is introduced. To illustrate and verify the procedure, experimental data (one-point and two-point) have been obtained with a laser Doppler system from a turbulent, round, free-air jet.     

Comparison of CCD,CMOS and intensified cameras

The properties of digital cameras are often important to obtain accurate results with image based measurement techniques. Unfortunately, a detailed comparison of the sensor specifications and performance is not accessible as this information is normally not provided by the manufacturers and no generally accepted comparison standard exists. Therefore, a detailed quantitative comparison was performed to evaluate and assess the characteristics of state-of-the-art CCD, CMOS and intensified CMOS sensors. These results may be of assistance when selecting the appropriate sensor for a desired application.