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145 results on '"Ma, Zhongjun"'

1. Human-level molecular optimization driven by mol-gene evolution

Author

Fang, Jiebin, Mao, Churu, Zhu, Yuchen, Chen, Xiaoming, Hsieh, Chang-Yu, and Ma, Zhongjun

Subjects
Computer Science - Machine Learning, Computer Science - Artificial Intelligence, Computer Science - Neural and Evolutionary Computing, Physics - Chemical Physics, Quantitative Biology - Biomolecules
Abstract

De novo molecule generation allows the search for more drug-like hits across a vast chemical space. However, lead optimization is still required, and the process of optimizing molecular structures faces the challenge of balancing structural novelty with pharmacological properties. This study introduces the Deep Genetic Molecular Modification Algorithm (DGMM), which brings structure modification to the level of medicinal chemists. A discrete variational autoencoder (D-VAE) is used in DGMM to encode molecules as quantization code, mol-gene, which incorporates deep learning into genetic algorithms for flexible structural optimization. The mol-gene allows for the discovery of pharmacologically similar but structurally distinct compounds, and reveals the trade-offs of structural optimization in drug discovery. We demonstrate the effectiveness of the DGMM in several applications.

Published
2024

25. Effect of joints on microwave fracturing of the Bukit Timah granite using an open‐ended antenna

Author

Ma, Zhongjun, Zheng, Yanlong, He, Lei, and Li, Jianchun

Abstract

Microwave fracturing of rocks before mechanical breakage could improve the performance of mechanical excavators and reduce environmental impacts. Previous research focused on the microwave fracturing of intact rock blocks. By using an open‐ended antenna, this paper investigates the effect of pre‐existing joints on the microwave fracturing of the Singapore Bukit Timah granite blocks. The results show that the specimens are weakened in the manners of cracking, spalling, melting, or a combination of them. The crack number and the total crack length produced by microwave treatment of jointed rock blocks are slightly smaller than those in the intact rock blocks. The interaction between joints and microwave‐induced cracks can be summarized into the following four patterns: (1) microwave‐induced cracks become arrested so that the crack propagation is terminated; (2) microwave‐induced cracks penetrate the joints and continue to propagate; (3) microwave‐induced cracks become deflected along the joints; and (4) microwave‐induced cracks propagate forward following the joints. The smaller the approach angle between the microwave‐induced crack and the pre‐existing joint is, the more microwave‐induced cracks tend to be arrested at the joint. Increasing the approach angle between the microwave‐induced crack and the joint can increase the chance of microwave‐induced crack penetrating the joint. The results also show that the smaller the distance is between the microwave radiation point and the joint, the easier it is for microwave‐induced cracks to penetrate the joints; otherwise, the microwave‐induced crack is more likely to be arrested at the pre‐existing joint. This study used an open‐ended microwave antenna to fracture the Bukit Timah granite at different dimensions. The effect of joints on microwave fracturing of the granite and the pattern of crack–joint interactions were systematically investigated.

Published
2022
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36. Global Exponential Stability of Periodic Oscillation for Nonautonomous BAM Neural Networks with Distributed Delay

Author

Ma Zhongjun, Wang Yi, and Liu Hongli

Subjects
Mathematics, QA1-939
Abstract

We derive a new criterion for checking the global stability of periodic oscillation of bidirectional associative memory (BAM) neural networks with periodic coefficients and distributed delay, and find that the criterion relies on the Lipschitz constants of the signal transmission functions, weights of the neural network, and delay kernels. The proposed model transforms the original interacting network into matrix analysis problem which is easy to check, thereby significantly reducing the computational complexity and making analysis of periodic oscillation for even large-scale networks.

Published
2009

49. <italic>Streptomyces nigra</italic> sp. nov. Is a Novel Actinobacterium Isolated From Mangrove Soil and Exerts a Potent Antitumor Activity <italic>in Vitro</italic>.

Author

Chen, Can, Ye, Yanghui, Wang, Ruijun, Zhang, Yinglao, Wu, Chen, Debnath, Sanjit C., Ma, Zhongjun, Wang, Jidong, and Wu, Min

Subjects
STREPTOMYCES, MANGROVE soils, ANTINEOPLASTIC agents
Abstract

A new bacterial strain, designated 452T, was isolated from the rhizosphere soil of the mangrove Avicennia marina in China. As determined, its cell wall peptidoglycan contained LL-diaminopimelic acid; MK-9(H8) and MK-9(H6) were the major isoprenoid quinones; and iso-C16:0 (31.3%), anteiso-C15:0 (16.9%), and iso-C15:0 (12.5%) were the major cellular fatty acids (>10.0%). Phylogenetic analysis based on the 16S rRNA gene sequence revealed that strain 452T formed a distinct lineage in the clade of the genus Streptomyces, and was closely related to S. coerulescens DSM 40146T (99.6% sequence identity), S. bellus DSM 40185T (99.5%), and S. coeruleorubidus DSM 41172T (99.3%). The DNA-DNA relatedness between strain 452T and these type strains ranged between 29.3 and 42.3%. Based on the phenotypic, chemotaxonomic, and phylogenetic features, the strain 452T is considered to represent a novel species of the genus Streptomyces, for which the name Streptomyces nigra sp. nov. is proposed. The type strain is 452T (=KCTC 39960T = MCCC 1K03346T). Further, strain 452T extracts exhibited a pronounced antitumor activity against human cancer cell lines A549, HCT-116, and HepG2, but not against normal human colon cells CCD-18Co. Active substances in the fermentation broth of strain 452T were isolated by bioassay-guided analysis, and then purified using a macroporous resin, silica gel, sephadex LX-20 column, and semi-preparative high-performance liquid chromatography (HPLC). Eight proline-containing diketopiperazines, namely, cyclo(Pro-Ala), cyclo(Pro-Gly), cyclo(Pro-Phe), cyclo(Pro-Met), cyclo(Pro-Val), cyclo(Pro-Leu), cyclo(Pro-Tyr), and cyclo(L-Leu-trans-4-hydroxy-L-Pro), were identified by electrospray ionization mass spectrometry (MS) and nuclear magnetic resonance (NMR). The compounds displayed different levels of cytotoxicity. The highest cytotoxicity was exhibited by cyclo(Pro-Ala) and cyclo(Pro-Met) against A549 cells, and cyclo(Phe-Pro) and cyclo(Pro-Ala) against HCT-116 cells, with average IC50 values equal to 18.5, 27.3, 32.3, and 47.6 μg/mL, respectively. The diversity of diketopiperazines and other chemicals produced by 452T was further investigated using gas chromatography (GC)-MS and liquid chromatography (LC)-MS. The analysis revealed 16 types of metabolites with antitumor activity and 16 other types of diketopiperazines. Hence, extracts of the newly identified strain may be used a starting material for the development of antitumor agents. [ABSTRACT FROM AUTHOR]

Published
2018
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