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.     

Synthesis and cytotoxicity of new 2-oxo-7-phenyl-2,3-dihydrothiazolo[4,5-b]pyridine-5-carboxylic acid amides

Abstract

The synthesis and anticancer activity evaluation of new thiazolo[4,5-b]pyridine-5-carboxylic acid amides is described. The structures of the synthesized compounds were confirmed by spectroscopic data and a single crystal X-ray diffraction analysis for 2.4. The synthesized compounds were screened for their in vitro anticancer activity according to US NCI protocols. The most active 7-(4-fluorophenyl)-2-oxo-2,3-dihydrothiazolo[4,5-b]pyridine-5-carboxylic acid (4-chlorophenyl)amide 2.2 and 7-(4-chlorophenyl)-2-oxo-2,3-dihydrothiazolo[4,5-b]pyridine-5-carboxylic acid (4-chlorophenyl)amide 2.5 were screened for their cytotoxicity effects on C6 Rat glioma cells and U373 Human glioblastoma astrocytoma cells which revealed promising results comparable to temozolamide as reference control according MTT assay data.     

A three‐dimensional Cartesian cut cell method for incompressible viscous flow with irregular domains

A three‐dimensional Cartesion cut cell method is presented for the simulations of incompressible viscous flows with irregular domains. A new model (referred to as ‘6+N’ model) is proposed to describe arbitrarily shaped cut cells and treat all the cells as polyhedrons with 6+N faces. The finite volume discretization of the Navier–Stokes equation is then implemented by using the ‘6+N’ model to separate the surface flux integrals into two parts, that is, the fluxes through the basic face of the hexahedron and those through the cutting surfaces. The previously proposed Kitta Cube algorithm and volume computer‐aided design platform (J. Comput. Aided. Des. 2005; 37(4): 1509–1520. Doi:10.1016/j.cad.2005.03.006) are adopted to generate cut cells and provide shape data and physical attributes for the numerical analysis. A modified SIMPLE‐based smoothing pressure correction scheme is applied to suppress checkerboard pressure oscillations caused by the collocated arrangement of velocities and pressure. The calculation accuracy of the numerical method expressed by L₁ and L _∞ norm errors is first demonstrated by the simulation of a pipe flow. Then its feasibility, efficiency, and potential in engineering applications are verified by applying it to solve natural convections between concentric spheres and between eccentric spheres. The heat transfer patterns in eccentric spheres are also obtained by using the numerical method. Copyright © 2011 John Wiley & Sons, Ltd.     

Side chain engineering of naphthalene diimide–bithiophene‐based polymer acceptors in all‐polymer solar cells

Two novel polymeric acceptors based on naphthalene diimide (NDI) and 2.2′‐bithiophene, named as P(NDI2THD‐T2) and P(NDI2TOD‐T2), were designed and synthesized for all polymer solar cells application. The structural and electronic properties of the two acceptors were modulated through side‐chain engineering of the NDI units. The optoelectronic properties of the polymers and the morphologies of the blend films composed of the polymer acceptors and a donor polymer PTB7‐Th were systemically investigated. With thiophene groups introduced into the side chains of the NDI units, both polymers showed wider absorption from 350 nm to 900 nm, compared with the reference polymer acceptor of N2200. No redshift of absorption spectra from solutions to films indicated reduced aggregation of the polymers due to the steric hindrance effect of thiophene rings in the side chains. The photovoltaic performance were characterized for devices in a configuration of ITO/PEDOT:PSS/PTB7‐Th:acceptors/2,9‐bis(3‐(dimethylamino)propyl)anthra[2,1,9‐def:6,5,10‐def]diisoquinoline‐1,3,8,10(2H,9H)‐tetraone (PDIN)/Al. With the addition of diphenyl ether as an additive, the power conversion efficiencies (PCEs) of 2.73% and 4.75% for P(NDI2THD‐T2) and P(NDI2TOD‐T2) based devices were achieved, respectively. The latter showed improved J_sc, Fill Factor (FF), and PCE compared with N2200 based devices. © 2017 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2017 , 55, 3679–3689     

Pd-Pt loaded graphene aerogel on nickel foam composite as binder-free anode for a direct glucose fuel cell unit

Fabrication of electrocatalyst for direct glucose fuel cell (DGFC) operation involves destructive preparation methods with the use of stabilizer like binder, which may cause activity depreciation. Binder-free electrocatalytic electrode becomes a possible solution to the above problem. Binder-free bimetallic Pd-Pt loaded graphene aerogel on nickel foam plates with different Pd/Pt ratios (1:2.32, 1:1.62, and 1:0.98) are successfully fabricated through a green one-step mild reduction process producing a Pd-Pt/GO/nickel form plate (NFP) composite. Anode with the binder-free electrocatalysts exhibit a strong activity in a batch type DGFC unit under room temperature. The effects of glucose and KOH concentrations, and the Pd/Pt ratios of the electrocatalyst on the DGFC performance are also studied. Maximum power density output of 1.25 mW cm⁻² is recorded with 0.5 M glucose/3 M KOH as the anodic fuel, and Pd₁Pt_0.98/GA/NFP as catalyst, which is the highest obtained so far among other types of electrocatalyst.     

BLEND MEMBRANES FOR DIRECT METHANOL AND PROTON EXCHANGE MEMBRANE FUEL CELLS

Sulphonated polystyrene ethylene butylene polystyrene(SPSEBS)prepared with 35%sulphonation was found to be highly elastic and enlarged up to 300%-400%of its initial length.It absorbed over 110%of water by weight.A major drawback of this membrane is its poor mechanical properties which are not adequate for use as polymer electrolytes in fuel cells.To overcome this,SPSEBS was blended with poly(vinylidene fluoride)(PVDF),a hydrophobic polymer.The blend membranes showed better mechanical properties than the base polymer.The effect of PVDF content on water uptake,ion exchange capacity and proton conductivity of the blend membranes was investigated.This paper presents the results of recent studies applied to develop an optimized in-house membrane electrode assembly(MEA)preparation technique combining catalyst ink spraying and assembly hot pressing.Easy steps were chosen in this preparation technique in order to simplify the method,aiming at cost reduction.The open circuit voltage for the cell with SPSEBS is 0.980 V which is higher compared to that of the cell with Nafion 117(0.790 V).From this study,it is concluded that a polymer electrolyte membrane suitable for proton exchange membrane fuel cell(PEMFC)and direct methanol fuel cell(DMFC)application can be obtained by blending SPSEBS and PVDF in appropriate proportions.The methanol permeability and selectivity showed a strong influence on DMFC performance.     

Degradation performance of polyglutamic acid and its application of calcium supplement

Degradable biopolymers with functional groups play a crucial role in the biomedical field. In this case, the influences of temperature and pH values on the degradation performance of poly (γ‐glutamic acid) (γ‐PGA) were fully explored by gel permeation chromatography. Further, γ‐PGA‐Ca was prepared by using calcium chloride to react with the low molecular weight γ‐PGA and characterized by Fourier transform infrared, differential scanning calorimetry test, gel permeation chromatography, atomic absorption spectrophotometric, Ca²⁺ release in vivo, and cytotoxicity experiments. Furthermore, Caco‐2 cell model was constructed to study the mechanism of γ‐PGA‐Ca intestinal absorption. Results indicated that low pH value and high temperature are the suitable conditions for the degradation of γ‐PGA. It also suggested that γ‐PGA‐Ca can be used as calcium supplements due to its high rate of absorption.     

Improvement of solar cell efficiency by applying Si3N4 nanopattern on glass substrate

A cylindrical Si₃N₄ nanopattern whose heights was 200 nm was fabricated on a glass substrate, and an aluminum-doped zinc oxide (AZO) layer was grown on the nanopatterned glass substrate. The nanopattern was applied to an amorphous silicon solar cell in order to increase the light-scattering effect, thus enhancing the efficiency of the solar cell. The reflectance of the solar cell on the Si₃N₄ nanopattern decreased and its absorption increased. Compared to a flat substrate, the short-circuit current density (J_sc) and conversion efficiency of a solar cell on the Si₃N₄ nanopatterned substrate were improved by 17.9% and 24.2%, respectively, as determined from solar simulator measurements.