Most recent issue published online in the International Journal of Data Mining and Bioinformatics.
International Journal of Data Mining and Bioinformatics
http://www.inderscience.com/browse/index.php?journalID=189&year=2024&vol=28&issue=1
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International Journal of Data Mining and Bioinformatics
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http://www.inderscience.com/browse/index.php?journalID=189&year=2024&vol=28&issue=1
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A data mining method for biomedical literature based on association rules algorithm
http://www.inderscience.com/link.php?id=136220
There are problems in the process of biomedical literature data mining, such as high data noise, low mining accuracy, and long-time consumption. Therefore, a biomedical literature data mining method based on association rule algorithm was designed. First, set up the extraction process of biomedical literature data, introduce the factor graph decomposition global extraction function, and establish a probabilistic database to speed up the extraction. Secondly, wavelet transform is used to denoise the data, improve the effectiveness of the extracted data, and classify it based on its importance. Finally, by setting association rules for biomedical literature data mining and introducing pre pruning methods on this basis, the time cost of calculating support is reduced, mining efficiency is improved, and combining confidence and dependency, a biomedical literature data mining model based on association rules is constructed to achieve the final mining. The results show that this method improves the accuracy of literature mining, reaching 99%, and effectively reduces the mining time, with a maximum time consumption of 1.7 seconds. It has strong application performance.
A data mining method for biomedical literature based on association rules algorithm
Xiaofeng Shi; Yaohong Zhao; Haijuan Du
International Journal of Data Mining and Bioinformatics, Vol. 28, No. 1 (2024) pp. 1 - 17
There are problems in the process of biomedical literature data mining, such as high data noise, low mining accuracy, and long-time consumption. Therefore, a biomedical literature data mining method based on association rule algorithm was designed. First, set up the extraction process of biomedical literature data, introduce the factor graph decomposition global extraction function, and establish a probabilistic database to speed up the extraction. Secondly, wavelet transform is used to denoise the data, improve the effectiveness of the extracted data, and classify it based on its importance. Finally, by setting association rules for biomedical literature data mining and introducing pre pruning methods on this basis, the time cost of calculating support is reduced, mining efficiency is improved, and combining confidence and dependency, a biomedical literature data mining model based on association rules is constructed to achieve the final mining. The results show that this method improves the accuracy of literature mining, reaching 99%, and effectively reduces the mining time, with a maximum time consumption of 1.7 seconds. It has strong application performance.]]>
10.1504/IJDMB.2024.136220
International Journal of Data Mining and Bioinformatics, Vol. 28, No. 1 (2024) pp. 1 - 17
Xiaofeng Shi
Yaohong Zhao
Haijuan Du
Centre of Modern Education Technology, Changchun Institute of Technology, Changchun, 130012, China ' Faculty of Computer Science and Technology, Changchun University, Changchun, 130022, China ' School of Information Science and Engineering, Jiaxing University, Jia'xing, 314001, China
association rules
biomedical literature
data mining
wavelet transform
vector space
classification basis
2024-01-22T23:20:50-05:00
Copyright © 2024 Inderscience Enterprises Ltd.
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17
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An in silico approach to de novo design of anti-microbial peptide from inspirited Komodo dragon's original VK6 peptide
http://www.inderscience.com/link.php?id=136225
Antimicrobial peptides (AMPs) function as the foremost barrier alongside fungi, bacteria, and viruses, thereby playing a pivotal role in innate immunity. These small peptides, ranging in size from 10 to 60 amino acid residues, are generated by various organisms. Reptiles, which are classified as ancient amniotes and have a wide range of ecological niches, are considered a valuable source of antimicrobial peptides (AMPs). In this study, we designed seven new AMPs to evaluate the impact of substituting tryptophan, phenylalanine, lysine, and arginine for enhancing antimicrobial activity using bioinformatic approaches. We assessed the relevant physicochemical traits using ProtParam and APD3 tools, and performed evaluations for possible allergenicity, antigenicity, and anti-inflammatory activity. The findings indicate that substitution of threonine, alanine, and valine amino acids in AMPs with tryptophan, phenylalanine, lysine, and arginine resulted in a noteworthy enhancement of the antimicrobial efficacy of the peptides designed, as compared to the original VK6 of Komodo dragon AMPs, accompanied by improved physicochemical properties. These findings highlight the applicability of bioinformatic tools in designing and optimising novel AMPs with increased antimicrobial activity, which could be a promising approach in combating multi-drug resistant bacteria.
An in silico approach to de novo design of anti-microbial peptide from inspirited Komodo dragon's original VK6 peptide
Milad Mohkam; Navid Nezafat; Younes Ghasemi
International Journal of Data Mining and Bioinformatics, Vol. 28, No. 1 (2024) pp. 18 - 39
Antimicrobial peptides (AMPs) function as the foremost barrier alongside fungi, bacteria, and viruses, thereby playing a pivotal role in innate immunity. These small peptides, ranging in size from 10 to 60 amino acid residues, are generated by various organisms. Reptiles, which are classified as ancient amniotes and have a wide range of ecological niches, are considered a valuable source of antimicrobial peptides (AMPs). In this study, we designed seven new AMPs to evaluate the impact of substituting tryptophan, phenylalanine, lysine, and arginine for enhancing antimicrobial activity using bioinformatic approaches. We assessed the relevant physicochemical traits using ProtParam and APD3 tools, and performed evaluations for possible allergenicity, antigenicity, and anti-inflammatory activity. The findings indicate that substitution of threonine, alanine, and valine amino acids in AMPs with tryptophan, phenylalanine, lysine, and arginine resulted in a noteworthy enhancement of the antimicrobial efficacy of the peptides designed, as compared to the original VK6 of Komodo dragon AMPs, accompanied by improved physicochemical properties. These findings highlight the applicability of bioinformatic tools in designing and optimising novel AMPs with increased antimicrobial activity, which could be a promising approach in combating multi-drug resistant bacteria.]]>
10.1504/IJDMB.2024.136225
International Journal of Data Mining and Bioinformatics, Vol. 28, No. 1 (2024) pp. 18 - 39
Milad Mohkam
Navid Nezafat
Younes Ghasemi
Allergy Research Center, Shiraz University of Medical Sciences, Shiraz, Iran ' Pharmaceutical Science Research Center, Shiraz University of Medical Sciences, Shiraz, Iran ' Pharmaceutical Science Research Center, Shiraz University of Medical Sciences, P.O. Box 71345-1583, Shiraz, Iran; Department of Pharmaceutical Biotechnology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
bioinformatics
in silico
Komodo dragon
antimicrobial peptides
AMPs
2024-01-22T23:20:50-05:00
Copyright © 2024 Inderscience Enterprises Ltd.
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39
2024-01-22T23:20:50-05:00
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A high precision recognition method for small area fingerprints based on machine vision
http://www.inderscience.com/link.php?id=136226
Aiming at the problem that the traditional small-area fingerprint recognition method is insufficient to recognise the feature points in the boundary region and the recognition accuracy is low, a high-precision small-area fingerprint recognition method based on machine vision is proposed. Firstly, by analysing the estimated values of key fingerprint parameters, Tico descriptor is introduced to obtain detailed feature points and determine the frequency field. Then, the fingerprint image of small area is enhanced based on direction and frequency to make the image features clearer. Then, based on the enhanced fingerprint image, the fingerprint model is demodulated by a suitable two-dimensional signal, the detailed features of the small-area fingerprint image are extracted, and the direction vector Angle is doubled to achieve direction smoothing, so as to achieve a better feature representation. Finally, high-precision identification of small area fingerprints is realised by matching the fingerprint point set. The experimental results show that the method proposed in this paper can extract the detailed features of small-area fingerprint images more accurately, the recognition results are more accurate, and the average recognition time is 32.6 s, which can improve the recognition efficiency, and has certain advantages.
A high precision recognition method for small area fingerprints based on machine vision
Qiqun Liu; Tan Liu
International Journal of Data Mining and Bioinformatics, Vol. 28, No. 1 (2024) pp. 40 - 57
Aiming at the problem that the traditional small-area fingerprint recognition method is insufficient to recognise the feature points in the boundary region and the recognition accuracy is low, a high-precision small-area fingerprint recognition method based on machine vision is proposed. Firstly, by analysing the estimated values of key fingerprint parameters, Tico descriptor is introduced to obtain detailed feature points and determine the frequency field. Then, the fingerprint image of small area is enhanced based on direction and frequency to make the image features clearer. Then, based on the enhanced fingerprint image, the fingerprint model is demodulated by a suitable two-dimensional signal, the detailed features of the small-area fingerprint image are extracted, and the direction vector Angle is doubled to achieve direction smoothing, so as to achieve a better feature representation. Finally, high-precision identification of small area fingerprints is realised by matching the fingerprint point set. The experimental results show that the method proposed in this paper can extract the detailed features of small-area fingerprint images more accurately, the recognition results are more accurate, and the average recognition time is 32.6 s, which can improve the recognition efficiency, and has certain advantages.]]>
10.1504/IJDMB.2024.136226
International Journal of Data Mining and Bioinformatics, Vol. 28, No. 1 (2024) pp. 40 - 57
Qiqun Liu
Tan Liu
School of Tourist Management, Henan Vocational College of Agriculture, Zhengzhou Henan, 451450, China ' School of Information Engineering, Henan Vocational College of Agriculture, Zhengzhou Henan, 451450, China
small area
fingerprints
high-precision
distinguish
machine vision
direction
frequency
2024-01-22T23:20:50-05:00
Copyright © 2024 Inderscience Enterprises Ltd.
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2024-01-22T23:20:50-05:00
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Uncovering the intension of Alisma orientale decoction for treating vertigo: a perspective from network analysis
http://www.inderscience.com/link.php?id=136230
<i>Alisma orientale decoction</i> (AOD), a traditional Chinese medicine composed of AO and AM, has a significant effect on the treatment of vertigo, improving the curative effect and reducing the likelihood of side effects with long-term stable medication. This manuscript established an interaction network between AOD and vertigo to explain, using network pharmacology, how AOD works to treat vertigo. Data mining of several databases yielded 12 candidate compounds, including eight components of AO and four components of AM, along with 331 potential targets. PPI analysis showed that the compounds acted mainly on key targets of MAPK1, EGFR, MAPK14, ERBB2, PIK3CA, MAPK8 and MTOR. In addition, GO and KEGG studies indicated that proteoglycans, ErbB signalling, HIF-1 signalling, chord metabolism, estrogen signalling, prolactin signalling and osteogenic class differentiation pathways were strongly involved in the signalling pathways of vertigo therapy. Data mining of the therapeutic targets and pathways provided new insights and considerations for drug development and clinical therapy of vertigo.
Uncovering the intension of Alisma orientale decoction for treating vertigo: a perspective from network analysis
Jing Huang; Lei Yang; Yizhen Lin
International Journal of Data Mining and Bioinformatics, Vol. 28, No. 1 (2024) pp. 58 - 72
<i>Alisma orientale decoction</i> (AOD), a traditional Chinese medicine composed of AO and AM, has a significant effect on the treatment of vertigo, improving the curative effect and reducing the likelihood of side effects with long-term stable medication. This manuscript established an interaction network between AOD and vertigo to explain, using network pharmacology, how AOD works to treat vertigo. Data mining of several databases yielded 12 candidate compounds, including eight components of AO and four components of AM, along with 331 potential targets. PPI analysis showed that the compounds acted mainly on key targets of MAPK1, EGFR, MAPK14, ERBB2, PIK3CA, MAPK8 and MTOR. In addition, GO and KEGG studies indicated that proteoglycans, ErbB signalling, HIF-1 signalling, chord metabolism, estrogen signalling, prolactin signalling and osteogenic class differentiation pathways were strongly involved in the signalling pathways of vertigo therapy. Data mining of the therapeutic targets and pathways provided new insights and considerations for drug development and clinical therapy of vertigo.]]>
10.1504/IJDMB.2024.136230
International Journal of Data Mining and Bioinformatics, Vol. 28, No. 1 (2024) pp. 58 - 72
Jing Huang
Lei Yang
Yizhen Lin
Fujian Provincial Key Laboratory of Ecology-Toxicological Effects and Control for Emerging Contaminants, Key Laboratory of Ecological Environment and Information Atlas (Fujian Provincial University), College of Environmental and Biological Engineering, Putian University, Zixiao East Road, Putian, Fujian, China ' Fujian Provincial Key Laboratory of Ecology-Toxicological Effects and Control for Emerging Contaminants, Key Laboratory of Ecological Environment and Information Atlas (Fujian Provincial University), College of Environmental and Biological Engineering, Putian University, Zixiao East Road, Putian, Fujian, China ' Fujian Provincial Key Laboratory of Ecology-Toxicological Effects and Control for Emerging Contaminants, Key Laboratory of Ecological Environment and Information Atlas (Fujian Provincial University), College of Environmental and Biological Engineering, Putian University, Zixiao East Road, Putian, Fujian, China
network pharmacology
Alisma orientale decoction
AOD
vertigo
Atractylodes macrocephala
2024-01-22T23:20:50-05:00
Copyright © 2024 Inderscience Enterprises Ltd.
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72
2024-01-22T23:20:50-05:00
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Exploring the pharmacological mechanism of Artemisia annua herba based on network pharmacology
http://www.inderscience.com/link.php?id=136231
This work focused on conducting pharmacological network analysis for identifying the mechanism of components of Artemisia annua herba (AAH) and corresponding target proteins related to cancer. We acquired chemical constituents of AAH based on traditional Chinese medicine systems pharmacology database (TCMSP), and obtained disease-related target-protein genes based on the comparative toxicogenomics database (CTD). A total of 18 AAH main active components such as Quercetin, Luteolin, Kaempferol, Isorhamnetin, etc., contained and 194 potential targets for cancer-related target proteins were identified. It mainly mediated pathways such as cancer, AGE-RAGE, IL-17, and TNF in the treatment of cancer, digestive system diseases, cardiovascular diseases, etc., by regulating 14 core targets such as TP53, RELA, RB1, NFKBIA, and MYC. Additionally, Cytoscape and STRING were applied in establishing the protein interaction networks. The present study established the new concept and method to develop and apply AAH by preliminary revealing the substance the basis and multi-dimensional pharmacological action mechanism of AAH, as well as reflecting its multi-component-multi-target-multi-way action features.
Exploring the pharmacological mechanism of Artemisia annua herba based on network pharmacology
Yuting Bai; Yulei Xie; Xiaowu Zhong; Can Luo; Qing Wu; Xin Chen
International Journal of Data Mining and Bioinformatics, Vol. 28, No. 1 (2024) pp. 73 - 90
This work focused on conducting pharmacological network analysis for identifying the mechanism of components of Artemisia annua herba (AAH) and corresponding target proteins related to cancer. We acquired chemical constituents of AAH based on traditional Chinese medicine systems pharmacology database (TCMSP), and obtained disease-related target-protein genes based on the comparative toxicogenomics database (CTD). A total of 18 AAH main active components such as Quercetin, Luteolin, Kaempferol, Isorhamnetin, etc., contained and 194 potential targets for cancer-related target proteins were identified. It mainly mediated pathways such as cancer, AGE-RAGE, IL-17, and TNF in the treatment of cancer, digestive system diseases, cardiovascular diseases, etc., by regulating 14 core targets such as TP53, RELA, RB1, NFKBIA, and MYC. Additionally, Cytoscape and STRING were applied in establishing the protein interaction networks. The present study established the new concept and method to develop and apply AAH by preliminary revealing the substance the basis and multi-dimensional pharmacological action mechanism of AAH, as well as reflecting its multi-component-multi-target-multi-way action features.]]>
10.1504/IJDMB.2024.136231
International Journal of Data Mining and Bioinformatics, Vol. 28, No. 1 (2024) pp. 73 - 90
Yuting Bai
Yulei Xie
Xiaowu Zhong
Can Luo
Qing Wu
Xin Chen
Department of Clinical Laboratory, Affiliated to Hospital of North Sichuan Medical College, Nanchong, 637000, China ' Department of Rehabilitation Medicine, Affiliated to Hospital of North Sichuan Medical College, Nanchong, 637000, China ' Department of Laboratory Medicine, North Sichuan Medical College, Nanchong, 637000, China ' Department of Rehabilitation Medicine, Affiliated to Hospital of North Sichuan Medical College, Nanchong, 637000, China ' Department of Rehabilitation Medicine, Affiliated to Hospital of North Sichuan Medical College, Nanchong, 637000, China ' Department of Rehabilitation Medicine, Affiliated to Hospital of North Sichuan Medical College, Nanchong, 637000, China
network pharmacology
mechanism
Artemisia annua herba
AAH
disease
2024-01-22T23:20:50-05:00
Copyright © 2024 Inderscience Enterprises Ltd.
28
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90
2024-01-22T23:20:50-05:00