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.     

Nucleophilic substitution of ferrocenyl alcohols catalyzed by bismuth(III) in aqueous medium at room temperature

A nucleophilic substitution reaction of an α‐ferrocenyl alcohol with various amines, indoles and thiols was successfully developed by using a catalytic amount of Bi(NO₃)₃.5H₂O at room temperature without the aid of phase transfer catalyst. The reactions proceeded in aqueous media, leading to the formation of new C=C, C=N and C=S bonds bearing ferrocenyl substituent with high efficiency. Copyright © 2012 John Wiley & Sons, Ltd.     

Analytical layer-element solutions of Biot’s consolidation with anisotropic permeability and incompressible fluid and solid constituents

Based on the governing equations of 2D plane-strain Biot’s consolidation, the relationship between generalized displacements and stresses of a single soil layer with anisotropic permeability and incompressible fluid and solid constituents is described by an analytical layer-element, which is deduced in the Laplace–Fourier transform domain by using the eigenvalue approach. Taking the boundary conditions and the continuity of the soil layers into consideration, a global stiffness matrix is subsequently assembled and solved. As to the 3D case, the same derivation is employed after the application of a decoupling transformation. The actual solutions in the physical domain can further be acquired by inverting the Laplace–Fourier transform. Finally, numerical examples are carried out to verify the presented theory and discuss the influence of the anisotropic permeability on the consolidation behavior.     

Study on detection of mutation DNA fragment in gastric cancer by restriction endonuclease fingerprinting with capillary electrophoresis

The DNA fragment detection focusing technique has further enhanced the sensitivity and information of DNA targets. The DNA fragment detection method was established by capillary electrophoresis with laser‐induced fluorescence detection and restriction endonuclease chromatographic fingerprinting (CE‐LIF‐REF) in our experiment. The silica capillary column was coated with short linear polyarclarylamide (SLPA) using nongel sieving technology. The excision product of various restricted enzymes of DNA fragments was obtained by REF with the molecular biology software Primer Premier 5. The PBR322/BsuRI DNA marker was used to establish the optimization method. The markers were focused electrophoretically and detected by CE‐LIF. The results demonstrate that the CE‐LIF‐REF with SLPA can improve separation, sensitivity and speed of analysis. This technique may be applied to analysis of the excision product of various restricted enzymes of prokaryotic plasmid (pIRES2), eukaryote plasmid (pcDNA3.1) and the PCR product of codon 248 region of gastric cancer tissue. The results suggest that this method could very sensitively separate the excision products of various restricted enzymes at a much better resolution than the traditional agarose electrophoresis. Copyright © 2011 John Wiley & Sons, Ltd.     

磁力平衡悬梁式液体界面张力仪的研制

液体界面张力系数是液体的重要物性参数之一,实现液体界面张力系数的精确测量具有重要的应用价值,所以我们以吊环法为基础开发出一套新型液体界面张力仪,该型仪器借助杠杆原理,利用霍尔式位移传感器以及永磁/电磁复合磁悬浮技术,通过对一个单摆式悬梁悬浮状态的监测和控制,将作用于金属吊环上的拉力适度放大并反映为电磁线圈的工作电流,进而实现液体界面张力的电法精确测量.所设计的仪器结构简单、测量精确、重复性好.     

Synthesis of Homoallylic Alcohols From Ketones in Water

Homoallylic alcohols have been prepared in good yields by allylation of ketones with allyl bromide in the presence of stannous chloride dihydrate, zinc iodide, and ammonium chloride in water.     

Analytic approximation of the blow‐up time for nonlinear differential equations by the ADM–Padé technique

We present a new approach to calculate analytic approximations of blow‐up solutions and their critical blow‐up times. Our approach applies the Adomian decomposition–Padé method to quickly and easily compute the critical blow‐up times, which comprises the Adomian decomposition method combined with the Padé approximants technique. We validate our new approach with a variety of numerical examples, including nonlinear ODEs, systems of nonlinear ODEs, and nonlinear PDEs. Furthermore, our new method is shown to be more convenient than prior art that relies on compound discretized algorithms. Copyright © 2013 John Wiley & Sons, Ltd.     

Chemical synthesis and characterization of manganese oxide coated Ni particles

Nanosized Ni particles with an average diameter of about 8 nm were prepared by reducing of NiCl 2 with sodium borohydride (NaBH 4 ) in aqueous solution. By moderate annealing in protective atmosphere, the composite grew up to be 15-20 nm particles. Both of the as-prepared and annealed Ni particles were coated by a layer of manganese oxide via decomposition reaction in aqueous KMnO4 solution. Hysteresis loops of as-prepared samples show a large increase in the magnetization with decreasing temperature and an unsaturated component at high magnetic field. In contrast, the ferromagnetic characteristics of annealed one are much stronger with large magnetization and coercivity. The thermomagnetic curves verified the coexistence of ferromagnetic Ni and antiferromangetic Mn oxide phases. But there exists no exchange bias behavior in the samples, even though the interface structure between the ferromagnetic Ni core and the antiferromagnetic manganese oxides has been distinctly formed. The absence of exchange bias probably originates from the weak ferromagnetic characteristic of Ni cores.     

Effects of ultra-strong magnetic field on electron capture rates of 55C0 and 56Ni in the magnetar surrounding

The electron capture rates of 55Co and 56Ni in the ultra-strong magnetic field at four typical temperature- density points have been calculated using the nuclear shell model and Landan energy levels quantized approximate correction. The results show that the electron capture rates of 55Co and 56Ni are increased greatly in the ultra-strong magnetic field, and even exceed two orders of magnitude in the range from 4.414×10^13G to 2.207×10^27 G. The change rate of electron abundance, ye, of 55Co and 56Ni under the condition of B=4.414×10^15G in the magnetar surrounding has been calculated and discussed, the proportions of ye of 55Co and 56Ni in the total Ye have been reduced by 50 percent in all more than the condition without a magnetic field.