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.     

Differential isotope dansylation labeling combined with liquid chromatography mass spectrometry for quantification of intact and N-terminal truncated proteins

The N-terminal amino acids of proteins are important structure units for maintaining the biological function, localization, and interaction networks of proteins. Under different biological conditions, one or several N-terminal amino acids could be cleaved from an intact protein due to processes, such as proteolysis, resulting in the change of protein properties. Thus, the ability to quantify the N-terminal truncated forms of proteins is of great importance, particularly in the area of development and production of protein-based drugs where the relative quantity of the intact protein and its truncated form needs to be monitored. In this work, we describe a rapid method for absolute quantification of protein mixtures containing intact and N-terminal truncated proteins. This method is based on dansylation labeling of the N-terminal amino acids of proteins, followed by microwave-assisted acid hydrolysis of the proteins into amino acids. It is shown that dansyl labeled amino acids are stable in acidic conditions and can be quantified by liquid chromatography mass spectrometry (LC–MS) with the use of isotope analog standards.     

Synthesis and Structural Characterization of Butadienylcalcium-based Heavy Grignard Reagents and a Ca4[O] Inverse Crown Ether Complex

The structure elucidation of heavy Grignard reagents (RAeX, Ae=Ca, Sr, and Ba, X=halides) has been greatly strived after, mainly because of their inaccessibility and remarkable instability. The synthesis of a series of butadienylcalcium compounds is presented, including 1-calcio-4-lithio-1,3-butadiene, 1,4-dicalcio-1,3-butadiene, and a Ca₄[O] inverse crown ether complex, via the reaction between 1,4-dilithio-1,3-butadienes and calcium iodide in THF. Single-crystal X-ray analysis of these unprecedented heavy Grignard reagents revealed unique structural characteristics and bonding modes. Preliminary reaction chemistry was investigated. This study provides a novel class of alkenyl heavy Grignard reagents and a useful synthetic strategy for otherwise unavailable reactive organometallic compounds.     

Analytical potential energy function and spectroscopy parameters for B~1Π state of KH

Multi-reference configuration interaction is used to produce potential energy curves(PECs) for the excited B1Π state of KH molecule.To investigate the correlation effect of core-valence electrons,five schemes are employed which include the different correlated electrons and different active spaces.The PECs are fitted into analytical potential energy functions(APEFs).The spectroscopic parameters,ro-vibrational levels,and transition frequencies are determined based on the APEFs and compared with available experimental and theoretical data.The molecular properties for B1Π obtained in this letter,which are better than those available in literature,can be reproduced with calculations using the suitable correlated electrons and active space of orbitals.     

Rapid determination of Pu isotopes for decommission concrete samples by inductively coupled plasma mass spectrometry

Journal of Radioanalytical and Nuclear Chemistry - Plutonium is one of the key radionuclides in nuclear decommission. In this study, a rapid method was developed to analyze Pu for concrete samples...     

Synthesis and Characterization of 1-Substituted - 1,2,3,4-Tetrahydro -9H-Pyrido[3,4-b]Indole-3-Carboxylic Acid Methyl Ester

以L-色氨酸甲酯盐酸盐为起始原料,经过Pictet-Spengler反应,再通过结晶诱导不对称转化(CIAT)过程,最后用饱和碳酸钠溶液脱除盐酸后高效选择性的得到1-取代-1,2,3,4-四氢-9H-吡啶并[3,4-b]吲哚-3-羧酸甲酯,目标产物通过重结晶或者柱层析方法纯化,所有化合物的结构均经元素分析,IR,1H NMR,13C NMR确证.     

Domino Radical Addition/Oxidation Sequence with Photocatalysis: One‐Pot Synthesis of Polysubstituted Furans from α‐Chloro‐Alkyl Ketones and Styrenes

A new domino reaction has been developed that allows the combination of styrenes and α‐alkyl ketone radicals to afford a wide array of polysubstituted furans in good to excellent yields under mild and simple reaction conditions. The key to success of this novel protocol is the use of photocatalyst fac‐Ir(ppy)₃ and oxidant K₂S₂O₈. Mechanistic studies by a radical scavenger and photoluminescence quenching suggest that a radical addition/oxidation pathway is operable.