New indoles from the roots of Brassica rapa ssp. campestris

Two new indoles, 2-C-β-D-glucopyranosyl-1-methoxyindole-3-acetonitrile (1) and 6-hydroxy-1-methylindole3-acetonitrile (2), along with two known indoles [caulilexin C (3) and arvelexin (4)], were isolated from turnip roots (Brassica rapa ssp. campestris L.). The structures of the compounds were established on the basis of NMR, FAB-MS, and IR spectroscopic data.     

Pore-Scale Analysis of NAPL Blob Dissolution and Mobilization in Porous Media

A pore-scale analysis of nonaqueous phase liquid (NAPL) blob dissolution and mobilization in porous media was presented. Dissolution kinetics of residual NAPLs in an otherwise water-saturated porous medium was investigated by conducting micromodel experiments. Changes in residual NAPL volume were measured from recorded video images to calculate the mass transfer coefficient, K and the lumped mass transfer rate coefficient, k. The morphological characteristics of the blobs such as specific and intrinsic area were found to be independent of water flow rate except at NAPL saturations below 2%. Dissolution process was also investigated by separating the mass transfer into zones of mobile and immobile water. The fractions of total residual NAPL perimeters in contact with mobile water and immobile water were measured and their relationship to the mass transfer coefficient was discussed. In general, residual NAPLs are removed by dissolution and mobilization. Although these two mechanisms were studied individually by others, their simultaneous occurrence was not considered. Therefore, in this study, mobilization of dissolving NAPL blobs was investigated by an analysis of the forces acting on a trapped NAPL blob. A dimensional analysis was performed to quantify the residual blob mobilization in terms of dimensionless Capillary number (Ca _I). If Ca _I is equal to or greater than the trapping number defined as , then blob mobilization is expected.     

Influence of imperfect elastic contact condition on the antiplane effective properties of piezoelectric fibrous composites

A fiber-reinforced periodic piezoelectric composite, where the constituents exhibit transverse isotropic properties, is considered. The fiber cross-section is circular and the periodicity is the same in two orthogonal directions. Imperfect mechanic contact conditions at the interphase between the matrix and fibers are represented in parametric form. In order to analyze the influence of the imperfect interface effect over the behavior of the composite, the effective axial piezoelectric moduli are obtained by means of the Asymptotic Homogenization Method. Some numerical examples are given.     

Unified formulae of variational bounds for multiphase anisotropic elastic composites

Using the spherical and deviator decomposition of the polarization and strain tensors, we present a general algorithm for the calculation of variational bounds of dimension d for any type of anisotropic linear elastic composite as a function of the properties of the comparison body. This procedure is applied in order to obtain analytical expressions of bounds for multiphase, linear elastic composites with cubic symmetry where the geometric shapes of the inclusions are arbitrary. For the validation, it can be proved that for the isotropic particular case, the bounds coincide with those recently reported by Gibiansky and Sigmund. On the other hand, based on this general procedure some, classical bounds reported by Hashin for transversely isotropic composites, are reproduced. Numerical calculations and some comparisons with other models and experimental data are shown.     

Innovative Freeze-Dried Snacks with Sodium Alginate and Fruit Pomace (Only Apple or Only Chokeberry) Obtained within the Framework of Sustainable Production

The aim of the work has been to develop freeze-dried fruit snacks in the form of bars with the use of by-products derived from fruit processing. In effect 14 product designs of fruit gels based on: apple pulp, apple juice, water, sodium alginate and only apple or only chokeberry pomace were prepared. The snacks were freeze-dried. The dry matter content, water activity, structure, colour, mechanical properties, as well as organoleptic evaluation were determined. Freeze-dried bares were obtained according to sustainability production which in this case was relied on application of fruit pomace. The freeze-drying process ensures the microbiological safety of the product without the need to use chemical preservatives. Freeze-dried samples obtained low water activity in the range of 0.099–0.159. The increase in pomace concentration (3–9%) boosted the dry matter content to above 98%, and decreased the brightness of the freeze-dried bars about 6 to 10 units. Mechanical properties varied depending on the product design. With the increase in the amount of pomace, the shear force increased at 23% to 41%. Based on the results, the best variant, that has the most delicate structure and the best organoleptic properties, has proven to contain 1% sodium alginate and 2% pomace.     

Mutual Support of Ligand- and Structure-Based Approaches—To What Extent We Can Optimize the Power of Predictive Model? Case Study of Opioid Receptors

The process of modern drug design would not exist in the current form without computational methods. They are part of every stage of the drug design pipeline, supporting the search and optimization of new bioactive substances. Nevertheless, despite the great help that is offered by in silico strategies, the power of computational methods strongly depends on the input data supplied at the stage of the predictive model construction. The studies on the efficiency of the computational protocols most often focus on global efficiency. They use general parameters that refer to the whole dataset, such as accuracy, precision, mean squared error, etc. In the study, we examined machine learning predictions obtained for opioid receptors (mu, kappa, delta) and focused on cases for which the predictions were the most accurate and the least accurate. Moreover, by using docking, we tried to explain prediction errors. We attempted to develop a rule of thumb, which can help in the prediction of compound activity towards opioid receptors via docking, especially those that have been incorrectly predicted by machine learning. We found out that although the combination of ligand- and structure-based path can be beneficial for the prediction accuracy, there still remain cases that cannot be reliably predicted by any available modeling method. In addition to challenging ligand- and structure-based predictions, we also examined the role of the application of machine-learning methods in comparison to simple statistical methods for both standard ligand-based representations (molecular fingerprints) and interaction fingerprints. All approaches were confronted in both classification (where compounds were assigned to the group of active and inactive group constructed on the basis of K_i values) and regression (where exact K_i value was predicted) experiments.     

Solvent-free,catalyst-free aza-Michael addition of cyclohexylamine to diethyl maleate: Reaction mechanism and kinetics

The aza-Michael reaction is the addition of an amine to an electron deficient C=C double bond. This reaction is also used in the synthesis of precursors of polymeric networks. In this study, we paid attention to the kinetics and mechanism of the aza-Michael addition of cyclohexylamine (CHXA) to diethyl maleate (DEM) performed as a solvent-free, catalyst-free reaction and to concurrent reactions. In situ Raman spectroscopy, NMR spectroscopy and gas chromatography/mass spectrometry have shown the occurrence of three simultaneous reactions: (i) the aza-Michael addition of CHXA to DEM leading to diethyl 2-(cyclohexylamino)succinate, (ii) isomerization of DEM to diethyl fumarate (DEF), and (iii) the aza-Michael addition of CHXA to DEF formed by the reaction (ii). All of these reactions proceed with third order kinetics, first order in DEM or DEF and second order in CHXA. We propose a kinetic model that allows kinetic constants to be estimated. Furthermore, a numerical solution of the set of differential equations confirms the expected kinetic equations of reactions (i) and (ii) and gives values of rate constants comparable to the estimated ones. A DFT mechanistic study illustrates the structure of the reaction intermediates and transition states of all reactions and explains the contribution of the second amine molecule in the reaction mechanism.     

Evidence for the isomerization and decarboxylation in the photoconversion of the red fluorescent protein DsRed

Recently, it has been shown that the red fluorescent protein DsRed undergoes photoconversion on intense irradiation, but the mechanism of the conversion has not yet been elucidated. Upon irradiation with a nanosecond-pulsed laser at 532 nm, the chromophore of DsRed absorbing at 559 nm and emitting at 583 nm (R form) converts into a super red (SR) form absorbing at 574 nm and emitting at 595 nm. This conversion leads to a significant change in the fluorescence quantum yield from 0.7 to 0.01. Here we demonstrate that the photoconversion is the result of structural changes of the chromophore and one amino acid. Absorption, fluorescence, and vibrational spectroscopy as well as mass spectrometry suggest that a cis-to-trans isomerization of the chromophore and decarboxylation of a glutamate (E215) take place upon irradiation to form SR. At the same time, another photoproduct (B) with an absorption maximum at 386 nm appears upon irradiation. This species is assigned as a protonated form of the DsRed chromophore. It might be a mixture of several protonated DsRed forms as there is at least two ways of formation. Furthermore, the photoconversion of DsRed is proven to occur through a consecutive two-photon absorption process. Our results demonstrate the importance of the chromophore conformation in the ground state on the brightness of the protein as well as the importance of the photon flux to control/avoid the photoconversion process.     

Laser techniques in acoustically levitated micro droplets

Laser techniques were applied to an acoustically levitated droplet for remote investigation of the diameter, species concentration and temperature of the suspended droplet. To this end, the third and the fourth harmonic of a Nd:YAG laser were used for investigation of elastic, fluorescence and phosphorescence signals from the droplet. The droplet was seeded with thermographic phosphors and acetone for the phosphorescence and fluorescence measurements, respectively. The techniques were applied simultaneously using an imaging stereoscope. The imaging device allowed for an identical visualization of incoming signal through separate optical filters. Temperature measurements in droplets is important in the study of e.g. exothermic chemical reactions, spray processes, combustion, and in bioanalytical applications where the biological material is temperature sensitive or dependent on optimal temperature for function. Results from these investigations showed that temperature measurements in acoustically levitated droplets using laser-induced phosphorescence are feasible. The results also show the potential of simultaneous laser based measurements on levitated droplets. Diameter variation (surface area), mixture concentration and temperature were measured simultaneously.