Using random forest to classify T-cell epitopes based on amino acid properties and molecular features

T-lymphocyte (T-cell) is a very important component in human immune system. T-cell epitopes can be used for the accurately monitoring the immune responses which activation by major histocompatibility complex (MHC), and rationally designing vaccines. Therefore, accurate prediction of T-cell epitopes is crucial for vaccine development and clinical immunology. In current study, two types peptide features, i.e., amino acid properties and chemical molecular features were used for the T-cell epitopes peptide representation. Based on these features, random forest (RF) algorithm, a powerful machine learning algorithm, was used to classify T-cell epitopes and non-T-cell epitopes. The classification accuracy, sensitivity, specificity, Matthews correlation coefficient (MCC), and area under the curve (AUC) values for proposed method are 97.54%, 97.22%, 97.60%, 0.9193, and 0.9868, respectively. These results indicate that current method based on the combined features and RF is effective for T-cell epitopes prediction.     

Improved λ/4 phase-shifted DFB semiconductor laser with spatial hole burning compensation using grating chirp

A λ/4 phase-shifted distributed feedback (DFB) semiconductor laser with a preformed chirped grating used to compensate the spatial hole burning (SHB) induced index change is proposed and analyzed. It shows that compared with the three phase shifted DFB laser which is known for its good performance to eliminate SHB, the proposed SHB compensated laser has better single longitudinal mode property, narrower spectral linewidth and better dynamic characteristics.     

Synthesis of S-monofluoromethyl phosphorothioates from PⅤ-H compounds and PhSO2SCH2F

S-Monofluoromethyl phosphorothioates represent an important class of organofluorine compounds and are re ported here for the first time.A series of S-monofluoromethyl phosphorothioates are conveniently synthesized from different P^Ⅴ-H compounds and PhSO₂SCH₂F under mild conditions.The method is compatible with common functional groups and provides potential opportunities to synthesize new bioactive molecules for medicinal chemistry.     

Spectroscopic and Binding Properties of Berberine to DNA and Its Application to DNA Detection

Berberine(BER) binds to the double helical DNA with a high affinity There is only a much smaller hypochromism and no shifts in the absorption spectra when BER binds to calf thymus DNA(CT DNA) The fluorescence yields increase dramatically when BER binds to DNA, with no shifts in the emission maximum. These spectral changes are in contrast to the behavior observed with many fluorescent intercalates Groove binding rather than intercalation was suggested to be the cause of these spectral changes. Consistent with groove binding, for polyamide anion quenching studies showed that the magnitude of K_sv of the bound BER was higher than that of the free BER. The addition of salt to the solution releases the DNA-bound drug action from the groove and causes a decrease in the fluorescence yield. The results of all above studies proved the groove binding of BER to DNA. The large fluorescence enhancements observed when BER binds to DNA and the poor fluorescence yield of BER in the absence of DNA can be used for sensitive detection of DNA The linear concentration range was 0–20μg/ml The limit of detection for CT DNA was 12 ng/ml     

Active-to-absorbing phase transition subjected to the velocity fluctuations in the frozen limit case

The directed bond percolation process is studied in the presence of compressible velocity fluctuations with long-range correlations. We discuss a construction of a field theoretic action and a way of obtaining its large scale properties using the perturbative renormalization group. The most interesting results for the frozen velocity limit are given.     

N-heterocyclic carbene-mediated formal [3+3] annulation of isatin-derived α, β-unsaturated acids: Access to functionalized 3,4′-spirooxindole δ-lactones

An in situ activation of isatin-derived α,β-unsaturated acids 2 for the generation of isatin-derived α,β-unsaturated acyl azoliums II was described. The acyl azoliums II were successfully applied to undergo a formal [3 + 3] annulation with 1,3-dicarbonyl compounds to access functionalized 3,4′-spirooxindole δ-lactones 4. A scale-up synthesis and an enantioselective variant of this protocol were also investigated. The stable and easily prepared acids 2 may be further utilized as promising versatile electrophilic 1,3-synthons for divergent synthesis of spirooxindoles.     

Angular-Multiplexing Optical Multiple-Image Encryption Based on Digital Holography and Random Amplitude Mask

We propose an improved optical image encryption scheme. By illuminating original images positioned in the input plane of the 4-f correlator and introducing reference waves with different incident angles in the output plane, we accomplish multiple-image encryption. To enhance the feasibility of the system and decrease the coding compliance for random phase mask, we apply the random amplitude masks and some digital manipulations in the encryption and decryption procedure. We also analyze the encryption and decryption quality of the method proposed together with the influence of different random number generators. Numerical simulation has proved the validity of the architecture suggested.     

Pollution characteristics and risk assessment of uranium and heavy metals of agricultural soil around the uranium tailing reservoir in Southern China

For the first time the pollution of the paddy soil within 2 km around the uranium tailing reservoir was investigated. The concentrations of U, Cd, Cr, Pb, Cu, Zn, Hg and As were determined by ICP-MS. The study showed that there was severe pollution in the first area (within 0–1 km of the tailing reservoir), which was caused by Cd, As, U and Hg. The pollution level of the second area (within 1–2 km) was relatively low. Hg and As were the main pollutants. In the first area, the contamination degree and risk of elements were positively correlated with the distance from the tailing reservoir. The second area was less polluted and influenced by mining and human activities because of mountain barriers.