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Qiao J, Wang G, Yang Z, Luo X, Chen J, Li K, Liu P. A hybrid particle swarm optimization algorithm for solving engineering problem. Sci Rep 2024; 14:8357. [PMID: 38594511 DOI: 10.1038/s41598-024-59034-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 04/05/2024] [Indexed: 04/11/2024] Open
Abstract
To overcome the disadvantages of premature convergence and easy trapping into local optimum solutions, this paper proposes an improved particle swarm optimization algorithm (named NDWPSO algorithm) based on multiple hybrid strategies. Firstly, the elite opposition-based learning method is utilized to initialize the particle position matrix. Secondly, the dynamic inertial weight parameters are given to improve the global search speed in the early iterative phase. Thirdly, a new local optimal jump-out strategy is proposed to overcome the "premature" problem. Finally, the algorithm applies the spiral shrinkage search strategy from the whale optimization algorithm (WOA) and the Differential Evolution (DE) mutation strategy in the later iteration to accelerate the convergence speed. The NDWPSO is further compared with other 8 well-known nature-inspired algorithms (3 PSO variants and 5 other intelligent algorithms) on 23 benchmark test functions and three practical engineering problems. Simulation results prove that the NDWPSO algorithm obtains better results for all 49 sets of data than the other 3 PSO variants. Compared with 5 other intelligent algorithms, the NDWPSO obtains 69.2%, 84.6%, and 84.6% of the best results for the benchmark function (f 1 - f 13 ) with 3 kinds of dimensional spaces (Dim = 30,50,100) and 80% of the best optimal solutions for 10 fixed-multimodal benchmark functions. Also, the best design solutions are obtained by NDWPSO for all 3 classical practical engineering problems.
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Affiliation(s)
- Jinwei Qiao
- School of Mechanical and Automotive Engineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250353, China
- Shandong Institute of Mechanical Design and Research, Jinan, 250353, China
| | - Guangyuan Wang
- School of Mechanical and Automotive Engineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250353, China
- Shandong Institute of Mechanical Design and Research, Jinan, 250353, China
| | - Zhi Yang
- School of Mechanical and Automotive Engineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250353, China.
- Shandong Institute of Mechanical Design and Research, Jinan, 250353, China.
| | - Xiaochuan Luo
- School of Information Science and Engineering, Northeastern University, Shenyang, 110819, China
| | - Jun Chen
- School of Mechanical and Automotive Engineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250353, China
- Shandong Institute of Mechanical Design and Research, Jinan, 250353, China
| | - Kan Li
- Fushun Supervision Inspection Institute for Special Equipment, Fushun, 113000, China
| | - Pengbo Liu
- School of Mechanical and Automotive Engineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250353, China
- Shandong Institute of Mechanical Design and Research, Jinan, 250353, China
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Tay Fernandez C. Making a Pangenome Using the Iterative Mapping Approach. Methods Mol Biol 2022; 2443:259-271. [PMID: 35037211 DOI: 10.1007/978-1-0716-2067-0_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Pangenomes have replaced single reference genomes as genetic references, as they contain a better scope of the diversity found in a single species. This protocol outlines the iterative mapping approach in constructing a pangenome, including how to check the raw data, align the data to a reference, how to assemble the data, and how to remove potential contaminants from the final assembly.
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Dan Q, Li Q, Li X, Suonan R, Dongzhi D, Guo X. Characterization of the complete chloroplast genome of the prickly blue poppy Meconopsis horridula Hook. f. & Thomson (Ranunculales: Papaveraceae). Mitochondrial DNA B Resour 2021; 6:792-793. [PMID: 33763580 PMCID: PMC7954420 DOI: 10.1080/23802359.2021.1882902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The prickly blue poppy (Meconopsis horridula Hook. f. & Thomson) is a traditional Tibetan medicinal herb with high values. In this study, its chloroplast genome was determined to be 153,761 bp in length with an A + T-biased base composition, and comprises a pair of inverted repeat (IR) regions (26,030 bp), separated by a large single-copy (LSC) region (83,803 bp) and a small single-copy (SSC) region (17,898 bp). A total of 113 gene species were annotated, with 20 of them being completely or partially duplicated and 18 of them harboring one or two introns. Phylogenetic analysis suggests that M. horridula is closely related to Meconopsis racemosa Maxim.
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Affiliation(s)
- Quehu Dan
- Tibetan Medicine Research Center, Tibetan Medical College, Qinghai University, Xining, PR China
| | - Qien Li
- Tibetan Medicine Research Center, Tibetan Medical College, Qinghai University, Xining, PR China.,State Key Laboratory of Tibetan Medicine Research and Development, Xining, PR China
| | - XianJia Li
- Tibetan Medicine Research Center, Tibetan Medical College, Qinghai University, Xining, PR China.,State Key Laboratory of Tibetan Medicine Research and Development, Xining, PR China
| | - Renqian Suonan
- Tibetan Medical Hospital of Qinghai Province, Xining, PR China
| | - Duojie Dongzhi
- State Key Laboratory of Tibetan Medicine Research and Development, Xining, PR China
| | - Xiao Guo
- Tibetan Medicine Research Center, Tibetan Medical College, Qinghai University, Xining, PR China.,State Key Laboratory of Tibetan Medicine Research and Development, Xining, PR China
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Li Q, Guo X, Yuan F, Nima C, Dongzhi D, Duojie, Li X. Characterization of the complete chloroplast genome of the Musk Larkspur Delphinium brunonianum (Ranunculales: Ranunculaceae). Mitochondrial DNA B Resour 2020; 5:2394-2396. [PMID: 33503075 PMCID: PMC7782922 DOI: 10.1080/23802359.2020.1775522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Musk Larkspur (Delphinium brunonianum) is a perennial herb of the family Ranunculace with medicinal values. In this study, the chloroplast (cp) genome of this herb was determined to be 153,926 bp long with an A + T-biased base composition, and comprises a pair of inverted repeat (IR) regions (26,559 bp), separated by a large single-copy (LSC) region (84,512 bp) and a small single-copy (SSC) region (16,296 bp). A total of 112 gene species were annotated with 19 of them being completely or partially duplicated. Eighteen gene species harbor one or two introns. Phylogenetic analysis challenged the monophyly of the subfamily Ranunculoideae.
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Affiliation(s)
- Qien Li
- Tibetan Medicine Research Center, Tibetan Medical College, Qinghai University, Xining, People's Republic of China.,State Key Laboratory of Tibetan Medicine Research and Development, Qinghai University, Xining, People's Republic of China
| | - Xiao Guo
- Tibetan Medicine Research Center, Tibetan Medical College, Qinghai University, Xining, People's Republic of China.,State Key Laboratory of Tibetan Medicine Research and Development, Qinghai University, Xining, People's Republic of China
| | - Farong Yuan
- Jinhe Tibetan Medicine Co., Ltd, Xining, People's Republic of China
| | - Cairang Nima
- State Key Laboratory of Tibetan Medicine Research and Development, Qinghai University, Xining, People's Republic of China
| | - Duojie Dongzhi
- State Key Laboratory of Tibetan Medicine Research and Development, Qinghai University, Xining, People's Republic of China
| | - Duojie
- State Key Laboratory of Tibetan Medicine Research and Development, Qinghai University, Xining, People's Republic of China
| | - XianJia Li
- Tibetan Medicine Research Center, Tibetan Medical College, Qinghai University, Xining, People's Republic of China.,State Key Laboratory of Tibetan Medicine Research and Development, Qinghai University, Xining, People's Republic of China
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Li Q, Li X, Qieyang R, Nima C, Dongzhi D, Duojie, Guo X. Characterization of the complete chloroplast genome of the Tangut monkshood Aconitum tanguticum (Ranunculales: Ranunculaceae). Mitochondrial DNA B Resour 2020; 5:2306-2307. [PMID: 33457769 PMCID: PMC7782905 DOI: 10.1080/23802359.2020.1773338] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
The Tangut monkshood (Aconitum tanguticum) is a perennial herb with high medicinal values. Here, its chloroplast genome was assembled from Illumina sequencing reads. The circular genome is 157,114 bp long with an A + T-biased nucleotide composition, and comprises a pair of inverted repeat (IR) regions (26,255 bp), separated by a large single-copy (LSC) region (87,559 bp) and a small single-copy (SSC) region (17,045 bp). It encodes a total of 112 gene species, with 19 of them being completely or partially duplicated and 18 of them harboring one or two introns. Phylogenetic analysis recovered two major clades of the genus Aconitum.
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Affiliation(s)
- Qien Li
- Tibetan Medicine Research Center, Tibetan Medical College, Qinghai University, Xining, People's Republic of China.,State Key Laboratory of Tibetan Medicine Research and Development, Qinghai University, Xining, People's Republic of China
| | - Xianjia Li
- Tibetan Medicine Research Center, Tibetan Medical College, Qinghai University, Xining, People's Republic of China.,State Key Laboratory of Tibetan Medicine Research and Development, Qinghai University, Xining, People's Republic of China
| | - Rangzhong Qieyang
- Tibetan Medicine Research Center, Tibetan Medical College, Qinghai University, Xining, People's Republic of China.,State Key Laboratory of Tibetan Medicine Research and Development, Qinghai University, Xining, People's Republic of China
| | - Cairang Nima
- State Key Laboratory of Tibetan Medicine Research and Development, Qinghai University, Xining, People's Republic of China
| | - Duojie Dongzhi
- State Key Laboratory of Tibetan Medicine Research and Development, Qinghai University, Xining, People's Republic of China
| | - Duojie
- State Key Laboratory of Tibetan Medicine Research and Development, Qinghai University, Xining, People's Republic of China
| | - Xiao Guo
- Tibetan Medicine Research Center, Tibetan Medical College, Qinghai University, Xining, People's Republic of China.,State Key Laboratory of Tibetan Medicine Research and Development, Qinghai University, Xining, People's Republic of China
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