Genome-wide association studies (GWAS) is an effective way to reveal the pathogenic genes of complex diseases by analyzing the genotype information and related disease phenotype information on the SNP loci of the whole genome of a large number of living organisms. Machine learning (ML) is a method that allows computers to simulate human cognitive processes to solve problems. The advantage of using machine learning methods to carry out genome-wide association analysis research is that it does not require false anchor points or gene-gene interaction models in advance Instead of exhaustive search, computer algorithms that simulate human cognitive processes can learn from a large amount of data to discover the ability of nonlinear high-dimensional gene-gene interactions. In recent years, a large number of machine learning methods have been used in the study of genome-wide association analysis. This article will briefly introduct these methods.
全基因组关联研究(genome -wide association studies, GWAS)是通过分析大量生物体全基因组SNP位点上的基因型信息和相关疾病表型信息，揭示复杂疾病致病基因的有效途径。机器学习(ML)是一种允许计算机模拟人类认知过程来解决问题的方法。利用机器学习方法开展全基因组关联分析研究的优势在于，它不需要事先建立假锚点或基因-基因相互作用模型，而是通过模拟人类认知过程的计算机算法，从大量数据中学习，发现非线性高维基因-基因相互作用的能力。近年来，大量的机器学习方法被用于全基因组关联分析的研究。本文将简要介绍这些方法。
{"title":"Overview of Machine Learning Methods for Genome-Wide Association Analysis","authors":"Minzhu Xie, Fang Liu","doi":"10.1145/3469678.3469682","DOIUrl":"https://doi.org/10.1145/3469678.3469682","url":null,"abstract":"Genome-wide association studies (GWAS) is an effective way to reveal the pathogenic genes of complex diseases by analyzing the genotype information and related disease phenotype information on the SNP loci of the whole genome of a large number of living organisms. Machine learning (ML) is a method that allows computers to simulate human cognitive processes to solve problems. The advantage of using machine learning methods to carry out genome-wide association analysis research is that it does not require false anchor points or gene-gene interaction models in advance Instead of exhaustive search, computer algorithms that simulate human cognitive processes can learn from a large amount of data to discover the ability of nonlinear high-dimensional gene-gene interactions. In recent years, a large number of machine learning methods have been used in the study of genome-wide association analysis. This article will briefly introduct these methods.","PeriodicalId":22513,"journal":{"name":"The Fifth International Conference on Biological Information and Biomedical Engineering","volume":"2 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-07-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"77108186","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
C2H2 zinc protein transcription family members play an important biological role in the mitotic bacteria. The study identified 25 and 26 families of C2H2 zinc dead, respectively, in Aspergillus flavus and Aspergillus oryzae genome databases. According to phytogenetics and fantasy analysis, the families of C2H2 zinc can be divided into four subfamilies. Genes in this family are distributed across eight chromosomes. In addition, the relationship of structure and function of C2H2 zinc transfer factors was comprehensively analyzed to intuitively understand the features of protective drawings. It also analyzed the expression profiles of the transcription factors of C2H2 under salt stress treatment and different growth phase. As a result, under salt stress treatment, C2H2 zinc has a relatively low algebraic and downward regulation of transcription factors. This work has a deeper understanding of the evolution and function of C2H2 zinc transcription factors in Aspergillus flavus and Aspergillus oryzae, and helps improve gene improvement of strains to adapt to complex surroundings.
{"title":"Identification of the C2H2 Type Zinc Finger Transcription Factor Family in Aspergillus Flavus and Aspergillus Oryzae and Their Expression Profiles in Aspergillus Oryzae","authors":"Qing Liu, Jianhua Huang, B. He","doi":"10.1145/3469678.3469693","DOIUrl":"https://doi.org/10.1145/3469678.3469693","url":null,"abstract":"C2H2 zinc protein transcription family members play an important biological role in the mitotic bacteria. The study identified 25 and 26 families of C2H2 zinc dead, respectively, in Aspergillus flavus and Aspergillus oryzae genome databases. According to phytogenetics and fantasy analysis, the families of C2H2 zinc can be divided into four subfamilies. Genes in this family are distributed across eight chromosomes. In addition, the relationship of structure and function of C2H2 zinc transfer factors was comprehensively analyzed to intuitively understand the features of protective drawings. It also analyzed the expression profiles of the transcription factors of C2H2 under salt stress treatment and different growth phase. As a result, under salt stress treatment, C2H2 zinc has a relatively low algebraic and downward regulation of transcription factors. This work has a deeper understanding of the evolution and function of C2H2 zinc transcription factors in Aspergillus flavus and Aspergillus oryzae, and helps improve gene improvement of strains to adapt to complex surroundings.","PeriodicalId":22513,"journal":{"name":"The Fifth International Conference on Biological Information and Biomedical Engineering","volume":"36 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-07-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"78041519","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
The multimode ablation which uses Radiofrequency heating after a pre-freezing process to treat the tumor, has shown significantly improved therapeutic effects and enhanced antitumor immune response. Unlike surgery, the ablated lesion remains in the body after treatment. Effective treatment evaluation is important to assess the immediate outcome and to monitor disease status over time. We proposed a novel postoperative assessment method combined radiomics features and thermal dose information. Patients with hepatocellular carcinoma and colorectal liver metastases from October 2016 to February 2019 were retrospectively studied. Based on the recorded parameters, intraoperative thermal dose distribution were constructed by a two-step "simulation-fusion" method, taking into account the superposition of energy from multiple treatments. Radiomic features of the tumor, such as grayscale, geometry and texture, were collected from preoperative and postoperative MRI, intraoperative CT and the thermal dose maps. The random survival forest model with input of clinical records, preoperative tumor features and intraoperative thermal dose features was the most competitive (C-index=0.92±0.012, iAUC=0.889, iBS=0.041). The grouping based on risk scores allows quick identification of the levels of long term risk after surgery. Based on the predicted survival probability function, clinicians can predictably enhance monitoring and perform other adjuvant therapies.
{"title":"Thermal Dose Images Enhance the Prediction of Local Tumor Progression After Multimode Ablation","authors":"Xinyi Wang, Jianlong Yang, A. Zhang, L. Xu","doi":"10.1145/3469678.3469694","DOIUrl":"https://doi.org/10.1145/3469678.3469694","url":null,"abstract":"The multimode ablation which uses Radiofrequency heating after a pre-freezing process to treat the tumor, has shown significantly improved therapeutic effects and enhanced antitumor immune response. Unlike surgery, the ablated lesion remains in the body after treatment. Effective treatment evaluation is important to assess the immediate outcome and to monitor disease status over time. We proposed a novel postoperative assessment method combined radiomics features and thermal dose information. Patients with hepatocellular carcinoma and colorectal liver metastases from October 2016 to February 2019 were retrospectively studied. Based on the recorded parameters, intraoperative thermal dose distribution were constructed by a two-step \"simulation-fusion\" method, taking into account the superposition of energy from multiple treatments. Radiomic features of the tumor, such as grayscale, geometry and texture, were collected from preoperative and postoperative MRI, intraoperative CT and the thermal dose maps. The random survival forest model with input of clinical records, preoperative tumor features and intraoperative thermal dose features was the most competitive (C-index=0.92±0.012, iAUC=0.889, iBS=0.041). The grouping based on risk scores allows quick identification of the levels of long term risk after surgery. Based on the predicted survival probability function, clinicians can predictably enhance monitoring and perform other adjuvant therapies.","PeriodicalId":22513,"journal":{"name":"The Fifth International Conference on Biological Information and Biomedical Engineering","volume":"20 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-07-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"87465394","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
SARS-CoV-2 caused atypical pneumonia (COVID-19) is an ongoing pandemic that seriously threat the global public health. Many people die from this disease with severe symptoms. The most prevalent m6A RNA modification may be involved in by assisting the virus escaping from the host cell immune system attack. We provided here the first computational prediction study of RNA methylation sites in SARS-CoV-2. Based on virus sequence information, we predict the potential virus m6A sites and hope to make anyhow contributions to this unprecedented situation. As a result, we found 27 most frequent m6A sequences (41 bp) in SARS-CoV-2, and two of them are quite near to the spike protein stop codon position.
{"title":"Computational Prediction of N6-methyladenosine (m6A) RNA Methylation in SARS-CoV-2 Viral Transcripts","authors":"Qingru Xu, Xiangyu Wu, Jia Meng","doi":"10.1145/3469678.3469689","DOIUrl":"https://doi.org/10.1145/3469678.3469689","url":null,"abstract":"SARS-CoV-2 caused atypical pneumonia (COVID-19) is an ongoing pandemic that seriously threat the global public health. Many people die from this disease with severe symptoms. The most prevalent m6A RNA modification may be involved in by assisting the virus escaping from the host cell immune system attack. We provided here the first computational prediction study of RNA methylation sites in SARS-CoV-2. Based on virus sequence information, we predict the potential virus m6A sites and hope to make anyhow contributions to this unprecedented situation. As a result, we found 27 most frequent m6A sequences (41 bp) in SARS-CoV-2, and two of them are quite near to the spike protein stop codon position.","PeriodicalId":22513,"journal":{"name":"The Fifth International Conference on Biological Information and Biomedical Engineering","volume":"97 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-07-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"85765328","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Chunxia Li, X. Kong, Minjia Wang, J. Yi, Jinghan Yi, Z. Deng, Qin Chen
Candida albicans is a common fungal pathogen, which is resistant to most commonly used disinfectants. It can cause serious interference in more than ten countries and even lead to death, so it is considered to be a serious global health threat. Obviously, in order to effectively control the spread of Candida albicans, the development of an efficient disinfectant is an important strategy. In this research, the fungicidal mechanism of ODB for Candida albicans was investigated through membrane fluidity, membrane integrity, protein leakage, functional changes of cell and mitochondria. ODB can affect fluidity and integrity of the cell membrane of Candida albicans, result in large amount of ions, proteins, glycerol, reactive oxygen species, ATP and DNA to leak, lower or dysfunction mitochondria by deteriorating cell ability to produce ATP or to make use of ATP, and less DNA content. And all these changes in structure and function are the main causes of the ultimate death of Candida albicans.
{"title":"Fungicidal Mechanism of Ortho-Phthaldialdehyde-benzyldlmethyldodecylammonlum Chloride as A Disinfectant Against Candida Albicans","authors":"Chunxia Li, X. Kong, Minjia Wang, J. Yi, Jinghan Yi, Z. Deng, Qin Chen","doi":"10.1145/3469678.3469710","DOIUrl":"https://doi.org/10.1145/3469678.3469710","url":null,"abstract":"Candida albicans is a common fungal pathogen, which is resistant to most commonly used disinfectants. It can cause serious interference in more than ten countries and even lead to death, so it is considered to be a serious global health threat. Obviously, in order to effectively control the spread of Candida albicans, the development of an efficient disinfectant is an important strategy. In this research, the fungicidal mechanism of ODB for Candida albicans was investigated through membrane fluidity, membrane integrity, protein leakage, functional changes of cell and mitochondria. ODB can affect fluidity and integrity of the cell membrane of Candida albicans, result in large amount of ions, proteins, glycerol, reactive oxygen species, ATP and DNA to leak, lower or dysfunction mitochondria by deteriorating cell ability to produce ATP or to make use of ATP, and less DNA content. And all these changes in structure and function are the main causes of the ultimate death of Candida albicans.","PeriodicalId":22513,"journal":{"name":"The Fifth International Conference on Biological Information and Biomedical Engineering","volume":"35 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-07-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"91343247","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Sleep apnea (SA) as abreathing disorder during sleep, has an increasing incidence in recent years. As a non-invasive method, heart rate variability (HRV) analysis can be effectively used in sleep apnea research. The information-based similarity of binary symbol sequence (BS_IBS) is a symbolic dynamics analysis method, which can be employed to perform nonlinear HRV analysis of sleep apnea patients. In the study, 60 electrocardiogram recordings were used for analysis, and multiple indices in time domain, frequency domain, and nonlinearity were calculated at the same. The similarity between adjacent RR segments was evaluated by calculating the BS_IBS value of them. Our research shows that BS_IBS is a useful sleep apnea screening method and can improve the effect of sleep apnea screening with traditional time-frequency domain indices (the accuracy is increased from 81.7% to 86.7%). This study proves that nonlinear information-based similarity assessment can be used in sleep apnea research and further expands the nonlinear HRV analysis method of sleep apnea.
{"title":"Information-Based Similarity of Binary Symbol Sequence as a New Index for Sleep Apnea Research","authors":"Shan Wu, Guanzheng Liu","doi":"10.1145/3469678.3469687","DOIUrl":"https://doi.org/10.1145/3469678.3469687","url":null,"abstract":"Sleep apnea (SA) as abreathing disorder during sleep, has an increasing incidence in recent years. As a non-invasive method, heart rate variability (HRV) analysis can be effectively used in sleep apnea research. The information-based similarity of binary symbol sequence (BS_IBS) is a symbolic dynamics analysis method, which can be employed to perform nonlinear HRV analysis of sleep apnea patients. In the study, 60 electrocardiogram recordings were used for analysis, and multiple indices in time domain, frequency domain, and nonlinearity were calculated at the same. The similarity between adjacent RR segments was evaluated by calculating the BS_IBS value of them. Our research shows that BS_IBS is a useful sleep apnea screening method and can improve the effect of sleep apnea screening with traditional time-frequency domain indices (the accuracy is increased from 81.7% to 86.7%). This study proves that nonlinear information-based similarity assessment can be used in sleep apnea research and further expands the nonlinear HRV analysis method of sleep apnea.","PeriodicalId":22513,"journal":{"name":"The Fifth International Conference on Biological Information and Biomedical Engineering","volume":"12 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-07-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"90301562","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Non-negative matrix factorization (NMF) is an effective technique for feature representation learning and dimensionality reduction. However, there are two critical challenges for improving the performance of NMF-based methods. One is the sparsity of representation, the other is the sensitivity to the initial value of the iteration, which seriously affects the performance of NMF. To solve the problems, L1/2 regularization is skillfully selected to characterize the sparsity of the data. Furthermore, a layer-wise pre-training strategy in deep learning is used to alleviate the effect of the initial value on NMF, whereby complex network structure is avoided. As such, a L1/2 regularization-based deep NMF (L1/2-DNMF) model is proposed in this study, such that a more stable and sparse deep representation is obtained. Moreover, incremental learning is introduced to reduce the high computational complexity of L1/2-DNMF model, called L1/2-DINMF model, which is suitable for online processing. Experiment results on genetic data-based tumor recognition verify that the proposed L1/2-DINMF model outperforms the classic and state-of-the-art methods.
{"title":"L1/2 Regularization-Based Deep Incremental Non-negative Matrix Factorization for Tumor Recognition","authors":"Lulu Yan, Xiaohui Yang","doi":"10.1145/3469678.3469691","DOIUrl":"https://doi.org/10.1145/3469678.3469691","url":null,"abstract":"Non-negative matrix factorization (NMF) is an effective technique for feature representation learning and dimensionality reduction. However, there are two critical challenges for improving the performance of NMF-based methods. One is the sparsity of representation, the other is the sensitivity to the initial value of the iteration, which seriously affects the performance of NMF. To solve the problems, L1/2 regularization is skillfully selected to characterize the sparsity of the data. Furthermore, a layer-wise pre-training strategy in deep learning is used to alleviate the effect of the initial value on NMF, whereby complex network structure is avoided. As such, a L1/2 regularization-based deep NMF (L1/2-DNMF) model is proposed in this study, such that a more stable and sparse deep representation is obtained. Moreover, incremental learning is introduced to reduce the high computational complexity of L1/2-DNMF model, called L1/2-DINMF model, which is suitable for online processing. Experiment results on genetic data-based tumor recognition verify that the proposed L1/2-DINMF model outperforms the classic and state-of-the-art methods.","PeriodicalId":22513,"journal":{"name":"The Fifth International Conference on Biological Information and Biomedical Engineering","volume":"70 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-07-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"74127249","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
A good understanding of the characteristics behavior of blood flow is significant for exploring the formation mechanism and process of atherosclerosis (AS), grasping the pathogenesis of AS, and providing effective theoretical guidance for clinical treatment of AS. To predict the influence of plaque on hemodynamics and the therapeutic effect of stent interventional treatment on stenosis artery, the coronary bifurcation models with/without stenosis and with stent implantation were constructed to analyze the hemodynamic characteristics in three cases using fluid-solid interaction method based on COMSOL software. The dynamic velocity, streamline, pressure, Von Mises stress, and displacement distributions in the coronary artery were obtained in these studies. Results show that the velocity of the plaque increased sharply, and the peripheral tissues of the plaque are more prone to the risk of injury because of the higher stress. The blood flow velocity tends to be stable in the stented artery and the velocity distribution is uniform, indicating that the blood supply of branch vessels is further improved, which is conducive to the normal blood supply and stable blood flow.
{"title":"Computation Prediction of the Therapeutic Effect of Metal Stent Implantation for Coronary Bifurcation","authors":"Xiaotong Yan, Kai Yue, Xinxin Zhang","doi":"10.1145/3469678.3469704","DOIUrl":"https://doi.org/10.1145/3469678.3469704","url":null,"abstract":"A good understanding of the characteristics behavior of blood flow is significant for exploring the formation mechanism and process of atherosclerosis (AS), grasping the pathogenesis of AS, and providing effective theoretical guidance for clinical treatment of AS. To predict the influence of plaque on hemodynamics and the therapeutic effect of stent interventional treatment on stenosis artery, the coronary bifurcation models with/without stenosis and with stent implantation were constructed to analyze the hemodynamic characteristics in three cases using fluid-solid interaction method based on COMSOL software. The dynamic velocity, streamline, pressure, Von Mises stress, and displacement distributions in the coronary artery were obtained in these studies. Results show that the velocity of the plaque increased sharply, and the peripheral tissues of the plaque are more prone to the risk of injury because of the higher stress. The blood flow velocity tends to be stable in the stented artery and the velocity distribution is uniform, indicating that the blood supply of branch vessels is further improved, which is conducive to the normal blood supply and stable blood flow.","PeriodicalId":22513,"journal":{"name":"The Fifth International Conference on Biological Information and Biomedical Engineering","volume":"23 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-07-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"74165465","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Zijie Wang, Yanlin Sun, Xiaoya Chi, Soon-Seong Hong
Grassland ecosystem is one of the indispensable ecosystem types in the world, accounting for approximately 30% of global land area. However, due to overgrazing and other human activities, grassland ecosystem is increasingly seriously degraded. Soil microorganism, as an important component of grassland soil ecology, plays a key role in litter decomposition, material metabolism and circulation. According to the results of large previous literature, soil microbial community structure could be affected by vegetation characteristics, soil properties and other environmental factors. Not surprisingly, soil microbial community structure could also be affected by different soil management strategies, including grazing intensity. As grazing could directly affect plant growth, soil porosity, nitrogen circulation and soil microbial community characteristics, the soil microbial community could be not only directly affected by grazing intensity, but also indirectly affected by the vegetation characteristics and soil properties that had changed with difference in grazing intensity. Therefore, there has been no unified conclusion about the effect of grazing intensity on soil microbial community. To further clarify this question, we utilized 16S amplifiers absolute quantitative sequencing technology to analyze the absolute abundance, diversity and composition of soil bacterial communities of Stipa grandis grasslands under different grazing intensity in Xilingol League, Inner Mongolia, China in this study. The correlations with soil bacterial communities and their corresponding environmental factors were also analyzed. Our results suggested that soil bacterial diversity decreased at first and then increased with the increase of grazing intensity, and the evenness had no significant variation with the difference in grazing intensity. Grazing intensity significantly affected the composition of soil bacterial communities at the phylum level: with the increase of grazing intensity, the abundance of Verrucomicrobia decreased at first and then increased, the abundance of Planctomycetes and Gemmatimonadetes significantly decreased, and the abundance of Nitrospirae significantly increased. According to the redundancy analysis with vegetation characteristics and soil properties, it indicated that the dominant soil bacterial phyla showed significant correlations with soil pH value, number of Gramineous species, aboveground biomass of Gramineous species, total aboveground biomass, soil organic matter content, available nitrogen content, available phosphorus and total nitrogen contents. This work could provide more scientific evidence for understanding of the effects of grazing intensity on soil bacterial community structure.
{"title":"Effects of Grazing Intensity on Soil Bacterial Community Structure of Stipa grandis Grasslands in Inner Mongolia, China","authors":"Zijie Wang, Yanlin Sun, Xiaoya Chi, Soon-Seong Hong","doi":"10.1145/3469678.3469700","DOIUrl":"https://doi.org/10.1145/3469678.3469700","url":null,"abstract":"Grassland ecosystem is one of the indispensable ecosystem types in the world, accounting for approximately 30% of global land area. However, due to overgrazing and other human activities, grassland ecosystem is increasingly seriously degraded. Soil microorganism, as an important component of grassland soil ecology, plays a key role in litter decomposition, material metabolism and circulation. According to the results of large previous literature, soil microbial community structure could be affected by vegetation characteristics, soil properties and other environmental factors. Not surprisingly, soil microbial community structure could also be affected by different soil management strategies, including grazing intensity. As grazing could directly affect plant growth, soil porosity, nitrogen circulation and soil microbial community characteristics, the soil microbial community could be not only directly affected by grazing intensity, but also indirectly affected by the vegetation characteristics and soil properties that had changed with difference in grazing intensity. Therefore, there has been no unified conclusion about the effect of grazing intensity on soil microbial community. To further clarify this question, we utilized 16S amplifiers absolute quantitative sequencing technology to analyze the absolute abundance, diversity and composition of soil bacterial communities of Stipa grandis grasslands under different grazing intensity in Xilingol League, Inner Mongolia, China in this study. The correlations with soil bacterial communities and their corresponding environmental factors were also analyzed. Our results suggested that soil bacterial diversity decreased at first and then increased with the increase of grazing intensity, and the evenness had no significant variation with the difference in grazing intensity. Grazing intensity significantly affected the composition of soil bacterial communities at the phylum level: with the increase of grazing intensity, the abundance of Verrucomicrobia decreased at first and then increased, the abundance of Planctomycetes and Gemmatimonadetes significantly decreased, and the abundance of Nitrospirae significantly increased. According to the redundancy analysis with vegetation characteristics and soil properties, it indicated that the dominant soil bacterial phyla showed significant correlations with soil pH value, number of Gramineous species, aboveground biomass of Gramineous species, total aboveground biomass, soil organic matter content, available nitrogen content, available phosphorus and total nitrogen contents. This work could provide more scientific evidence for understanding of the effects of grazing intensity on soil bacterial community structure.","PeriodicalId":22513,"journal":{"name":"The Fifth International Conference on Biological Information and Biomedical Engineering","volume":"61 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-07-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"73888402","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Objective: To tentatively investigate the mechanism of uncaria rhynchophylla (UR) in treatment of Alzheimer's disease (AD). Methods: The targets and pathways of UR against AD were obtained from network pharmacology analysis. Results: We analyzed and obtained 7 active ingredients of UR, 29 targets of UR for treatment of AD, of which 26.9% targets were protein-modifying enzymes. The core active ingredients of UR were C3, C6, C7 and C5. The core targets of UR in the treatment of AD are AKT1, CASP3 and MTOR. The enrichment analysis of GO biological process suggests that the biological function of UR in the treatment of AD mainly involves regulation of neurotransmitter levels, rhythmic process, cellular response to nitrogen compound, calcium ion transport, response to toxic substance, response to oxygen levels, maintenance of location, positive regulation of cell death, and apoptotic signaling pathway, etc. KEGG pathway enrichment analysis showed that the most significant enrichment signaling pathways were neuroactive ligand-receptor interaction, calcium signaling pathway, cAMP signaling pathway, PI3K-Akt signaling pathway and so on. Conclusion: UR against AD may be related to its multiple components, multiple targets and biological functions. This study can provide a theoretical basis for further experimental and clinical research.
{"title":"Use Chou's 5-steps Rule to Study the Mechanism of Uncaria Rhynchophylla for Treating Alzheimer's Disease Based on Network Pharmacology","authors":"Meng Fang, Peng Zeng, Jinglou Chen, Han Zhao, Haiping Wang, Jing Guo","doi":"10.1145/3469678.3469695","DOIUrl":"https://doi.org/10.1145/3469678.3469695","url":null,"abstract":"Objective: To tentatively investigate the mechanism of uncaria rhynchophylla (UR) in treatment of Alzheimer's disease (AD). Methods: The targets and pathways of UR against AD were obtained from network pharmacology analysis. Results: We analyzed and obtained 7 active ingredients of UR, 29 targets of UR for treatment of AD, of which 26.9% targets were protein-modifying enzymes. The core active ingredients of UR were C3, C6, C7 and C5. The core targets of UR in the treatment of AD are AKT1, CASP3 and MTOR. The enrichment analysis of GO biological process suggests that the biological function of UR in the treatment of AD mainly involves regulation of neurotransmitter levels, rhythmic process, cellular response to nitrogen compound, calcium ion transport, response to toxic substance, response to oxygen levels, maintenance of location, positive regulation of cell death, and apoptotic signaling pathway, etc. KEGG pathway enrichment analysis showed that the most significant enrichment signaling pathways were neuroactive ligand-receptor interaction, calcium signaling pathway, cAMP signaling pathway, PI3K-Akt signaling pathway and so on. Conclusion: UR against AD may be related to its multiple components, multiple targets and biological functions. This study can provide a theoretical basis for further experimental and clinical research.","PeriodicalId":22513,"journal":{"name":"The Fifth International Conference on Biological Information and Biomedical Engineering","volume":"27 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-07-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"84272991","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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