DeepNGlyPred: A Deep Neural Network-Based Approach for Human N-Linked Glycosylation Site Prediction

Protein N-linked glycosylation is a post-translational modification that plays an important role in a myriad of biological processes. Computational prediction approaches serve as complementary methods for the characterization of glycosylation sites. Most of the existing predictors for N-linked glycosylation utilize the information that the glycosylation site occurs at the N-X-[S/T] sequon, where X is any amino acid except proline. Not all N-X-[S/T] sequons are glycosylated, thus the N-X-[S/T] sequon is a necessary but not sufficient determinant for protein glycosylation. In that regard, computational prediction of N-linked glycosylation sites confined to N-X-[S/T] sequons is an important problem. Here, we report DeepNGlyPred a deep learning-based approach that encodes the positive and negative sequences in the human proteome dataset (extracted from N-GlycositeAtlas) using sequence-based features (gapped-dipeptide), predicted structural features, and evolutionary information. DeepNGlyPred produces SN, SP, MCC, and ACC of 88.62%, 73.92%, 0.60, and 79.41%, respectively on N-GlyDE independent test set, which is better than the compared approaches. These results demonstrate that DeepNGlyPred is a robust computational technique to predict N-Linked glycosylation sites confined to N-X-[S/T] sequon. DeepNGlyPred will be a useful resource for the glycobiology community.     

Magnetic nanoparticles and concentrated magnetic nanofluids： Synthesis, properties and some applications

This paper reviews some recent results concerning chemical synthesis of magnetic nanoparticles and preparation of various types of magnetic nanofluids. Structural properties and behaviour in external magnetic field of magnetic nanofluids will be emphasized with relation to their use in leakage-free rotating seals and in biomedical applications.     

Solving systems of equivalentions

We obtain a property of distributivity in the equivalence form overLR fuzzy intervals. As an application and main result of the paper, we give a determinant method to solve systems of linear equivalentions. The expected value of the obtained solution is equal to the corresponding solution of the classical system of linear equations considering the expected values as data.     

Apriori error estimation in terms of the third derivative for the method of successive approximations applied to ODE’S

Here we present a new apriori error estimation for the method of successive approximations applied to ODE’s, using a perturbed trapezoidal quadrature rule. This estimation holds for functions which have continuous and Lipschitzian third order derivatives.     

Intense laser effects on the optical properties of asymmetric GaAs double quantum dots under applied electric field

We investigated the combined effects of a non-resonant intense laser field and a static electric field on the electronic structure and the nonlinear optical properties (absorption, optical rectification) of a GaAs asymmetric double quantum dot under a strong probe field excitation. The calculations were performed within the compact density-matrix formalism under steady state conditions using the effective mass approximation. Our results show that: (i) the electronic structure and optical properties are sensitive to the dressed potential; (ii) under applied electric fields, an increase of the laser intensity induces a redshift of the optical absorption and rectification spectra; (iii) the augment of the electric field strength leads to a blueshift of the spectra; (iv) for high electric fields the optical spectra show a shoulder-like feature, related with the occurrence of an anti-crossing between the two first excited levels.     

Pharmaceutically active ionic liquids with solids handling, enhanced thermal stability, and fast release

Pharmaceutically active compounds in ionic liquid form immobilized onto mesoporous silica are stable, easily handled solids, with fast and complete release from the carrier material when placed into an aqueous environment. Depending on specific ion-surface interactions, they may also exhibit improved thermal stability when compared to the non-adsorbed compounds.     

Removal of uranyl ions from UO2(NO3)2 solution by means of Chlorella vulgaris and Dunaliella salina algae

This paper deals with a study of the biosorption of UO₂ ²⁺ ions on two green algae: Chlorella vulgaris and Dunaliella salina. By investigating the retention degree versus contact time from Langmuir and Freundlich biosorption isotherms, kinetic investigations and FTIR spectra it was found that the biosorption process was greater for Chlorella vulgaris than for Dunaliella salina. A new kinetics method is proposed to establish the reaction order concerning the biosorption process of uranyl ions on these biomasses.      

Interaction of (hydroxypropyl) cellulose with anionic surfactants in dilute regime

(Hydroxypropyl)cellulose (HPC) dilute aqueous solutions in the presence of sodium cholate (CS), sodium deoxycholate (DC), and sodium dodecylsulphate (SDS) were investigated. The hydrophobicity parameter (I ₁/I ₃) from fluorescence has shown a critical aggregation concentration (CAC) lower than the critical micellar concentration (CMC). One or two breakpoints were observed in the curve conductivity vs surfactant concentration. The thermodynamic parameters of aggregation (, and ) and the degree of counterion dissociation were calculated. Evidences for the secondary aggregation of CS/water system were found. The relative viscosity increases for HPC/bile salt solutions only at high surfactant concentrations, whereas for HPC/SDS, it passes through a maximum. The cloud points of both HPC/bile salt solutions at higher surfactant concentrations reach a temperature plateau value around 324 K, while for HPC/SDS, it exceeds 373 K at low SDS concentrations. Dynamic light scattering has demonstrated that the surfactants bind to HPC already at concentrations lower than CAC.Electronic Supplementary Material Supplementary material is available for this article at and is accessible for authorized users.     

Comparative analysis of the structure of sterically stabilized ferrofluids on polar carriers by small-angle neutron scattering

Results of experiments on small-angle neutron scattering from ferrofluids on polar carriers (pentanol, water, methyl-ethyl-ketone), with double-layer sterical stabilization of magnetic nanoparticles, are reported. Several types of spatial structural organization are observed. The structure of highly stable pentanol-based samples is similar to that of stable ferrofluids based on organic non-polar carriers (e.g., benzene) with mono-layer covered magnetic nanoparticles. At the same time, the effect of the interparticle interaction on the scattering is stronger in polar ferrofluids because of the structural difference in the surfactant shell. The structure of the studied methyl-ethyl-ketone- and water-based ferrofluids essentially different from the previous case. The formation of large (>100 nm in size) elongated or fractal aggregates, respectively, is detected even in the absence of external magnetic field, which corresponds to weaker stability of these types of ferrofluids. The structure of the fractal aggregates in water-based ferrofluids does not depend on the particle concentration, but it is sensitive to temperature. A temperature increase results in a decrease in their fractal dimension reflecting destruction of the aggregates. In addition, in water-based ferrofluids these aggregates consist of small (radius approximately 10 nm) and temperature-stable primary aggregates.