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multivariate statistical analysis of Large Datasets: Single Particle Electron Microscopy

Open Journal of Statistics 2016年第4期6卷 701-739页

作者： Marin van Heel Rodrigo V. Portugal Michael Schatz Institute of Biology Leiden Leiden University NeCEN Leiden The Netherlands Sir Ernst Chain Building Imperial College London London UK Brazilian Nanotechnology National Laboratory CNPEM Campinas Brazil Image Science Software GmbH Berlin Germany

Biology is a challenging and complicated mess. Understanding this challenging complexity is the realm of the biological sciences: Trying to make sense of the massive, messy data in terms of discovering patterns and revealing its underlying general rules. Among the most powerful mathematical tools for organizing and helping to structure complex, heterogeneous and noisy data are the tools provided by multivariate statistical analysis (MSA) approaches. These eigenvector/eigenvalue data-compression approaches were first introduced to electron microscopy (EM) in 1980 to help sort out different views of macromolecules in a micrograph. After 35 years of continuous use and developments, new MSA applications are still being proposed regularly. The speed of computing has increased dramatically in the decades since their first use in electron microscopy. However, we have also seen a possibly even more rapid increase in the size and complexity of the EM data sets to be studied. MSA computations had thus become a very serious bottleneck limiting its general use. The parallelization of our programs—speeding up the process by orders of magnitude—has opened whole new avenues of research. The speed of the automatic classification in the compressed eigenvector space had also become a bottleneck which needed to be removed. In this paper we explain the basic principles of multivariate statistical eigenvector-eigenvalue data compression;we provide practical tips and application examples for those working in structural biology, and we provide the more experienced researcher in this and other fields with the formulas associated with these powerful MSA approaches.

关键词： Single Particle Cryo-EM multivariate statistical analysis Unsupervised Classification Modulation Distance Manifold Separation

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Chemical comparison of dried rehmannia root and prepared rehmannia root by UPLC-TOF MS and HPLC-ELSD with multivariate statistical analysis

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Acta Pharmaceutica Sinica B 2013年第1期3卷 55-64页

作者： Qiande Liang Jing Ma Zengchun Ma Yuguang Wang Hongling Tan Chengrong Xiao Ming Liu Beibei Lu Boli Zhang Yue Gao Institute of Radiation Medicine Academy of Military Medical ScienceBeijing 100850China Tianjin University of Traditional Chinese Medicine Tianjin 300193China

To identify the chemical differences which lead to the different therapeutic effects of dried rehmannia root(DRR)and prepared rehmannia root(PRR),we compared the chemical composition of decoctions of randomly purchased DRR and PRR using ultra performance liquid chromatography(UPLC)coupled with time-of-fight mass spectrometry and high performance liquid chromatography(HPLC)coupled with evaporative light scattering detection(ELSD)with the aid of multivariate statistical analysis.Both approaches clearly revealed compositional and quantitative differences between DRR and PRR.UPLC-MS data indicated stachyose,rehmaiono-side A(or rehmaionoside B),acteoside(or forsythiaside,or isoacteoside),6-O-coumaroylajugol(or 6-O-E-feruloylajugol,or 6-O-Z-feruloylajugol)as important discriminators between DRR and PRR decoctions.HPLC-ELSD analysis showed that the content of fructose in the decoctions of PRR was about four times greater than that of DRR(P<10^(-5)),while sucrose content in the decoctions of PRR was only about one seventh of that in DRR(P<0.01).Our results suggest that some compounds,such as fructose,stachyose and rehmaionoside,may be responsible for the differing therapeutic effects of DRR and PRR.Furthermore,improvements in quality control for PRR,which is currently lacking in the Chinese Pharmacopoeia,are recommended.

关键词： Rehmannia root Liquid chromatography Mass spectrometry Evaporated light scattering detection multivariate statistical analysis

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Rapid analysis and Identification of Absorbed Components and Their Metabolites of Yuanhu Zhitong Dropping Pill in Rat Plasma and Brain Tissue Using UPLC-Q-TOF/MS with multivariate statistical analysis

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Chinese Herbal Medicines 2016年第2期8卷 154-163页

作者： Hong-bing Zhang Tie-jun Zhang Jun Xu Xi-min Zhang Ya-zhuo Li Chang-xiao Liu School of Chinese Materia Medica Tianjin University of Traditional Chinese Medicine State Key Laboratory of Drug Delivery Technology and Pharmacokinetics Tianjin Institute of Pharmaceutical Research Gansu Longshenrongfa Pharmaceutical Co. Ltd.

Objective To establish an effective approach for rapid and comprehensive analysis on the absorbed and metabolic components in rats after ig administration of Yuanhu Zhitong Dropping Pill（YHZT）. Methods Based on the combination of UPLC-Q-TOF/MS and multivariate statistical analysis, the absorbed prototype constituents and their metabolites in rat plasma were rapidly analyzed and identified, and the components absorbed into brain were further identified by comparing the extracted ion chromatograms（EICs） of control and brain tissue samples of dosed rats. Results A total of 38 YHZT-related xenobiotic compounds were detected and identified as the potential bioactive constituents in rat plasma, including 24 absorbed prototype constituents and 14 metabolites. In particular, of all prototype constituents, 14 were also detected in rat brain tissue, indicating that they could penetrate the blood-brain barrier and enter into brain. Conclusion An effective method is established and applied to analyze the potential bioactive constituents in YHZT, which provides a pathway to further investigate the pharmacological pattern and mechanism of YHZT.

关键词： metabolites multivariate statistical analysis prototype constituents UPLC-Q-TOF/MS Yuanhu Zhitong Dropping Pill

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Quality assessment of Jinhongtang Granule using UFLC-MS/MS and multivariate statistical analysis

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Asian Journal of Traditional Medicines 2021年第4期16卷 191-202页

作者： Fan Wu Yu Zhang Yanling Qiao Ting Zhao Baojing Zhang Bangjiang Fang Xiaokui Huo Xiaochi Ma Institute of Integrative Medicine College of PharmacyThe Second Affiliated HospitalDalian Medical UniversityDalian 116044China Department of Emergency LongHua HospitalShanghai University of Traditional Chinese MedicineShanghai 200032China

Jinhongtang is a traditional Chinese medicine formula composed of Rheum palmatum L.stem,Sargentodoxa cuneata stem,and Taraxacum mongolicum and is used for the treatment of sepsis.However,quality assessment method for Jinhongtang is not available.In present study,we developed a UFLC-MS/MS method to determine 16 analytes in 20 batches of home-made and commercial Jinhongtang.multivariate statistical analysis revealed the significant differences in the quality of home-made and commercial Jinhongtang and the difference in the quality of home-made samples was more significant.The integrated strategy based on UFLC-MS/MS and multivariate statistical analysis provided a new basis for the overall quality assessment of Jinhongtang.

关键词： Jinhongtang quality assessment UFLC-MS/MS multivariate statistical analysis

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Study on the Relationship between Soil and Environment Based on multivariate statistical analysis

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Meteorological and Environmental Research 2012年第5期3卷 1-3,8页

作者： DONG Li-li College of Tourism Resources and EnvironmentXianyang Normal UniversityXianyang 712000China

[Objective] The study aimed to study the relationship between soil and environment on the basis of multivariate statistical analysis. [ Method] Through field investigation, sampling and laboratory analysis, we discussed the relationship between soil properties and environmental factors in Mizhi County, North Shaanxi by using Canoco multivariate statistical analysis. [ Result]According to the effects of various environmental factors on soil properties, the influencing order of environmental factors was land use way 〉 vegetation type 〉 vegetation restoration years 〉 vegeta- tion coverage 〉 slope aspect 〉 gradient 〉 elevation. In a word, soil properties were significantly affected by land use way and vegetation type which were the most important environmental factors of soil properties in spatial variation, while vegetation restoration years were closely related to the ac- cumulation of soil nutrients. [ Condusion]The research could provide theoretical references for the construction of ecological environment in Loess Plateau of China.

关键词： Soil properties multivariate statistical analysis Land use Vegetation types China

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Characteristics and genesis of groundwater salinization in coastal areas of the Lower Reaches of Oujiang Basin

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Journal of Groundwater Science and Engineering 2024年第2期12卷 190-204页

作者： Mei-hui Zhang Shi-yang Zhou Dan-dan Liu Ying Zhang Yu-xi Zhang Xi Chen Hui-wei Wang Bei Li Wei Kang Bing Yi Wan-peng Shi Institute of Hydrogeology and Environmental Geology Chinese Academy of Geological SciencesShijiazhuang 050061China Fujian Provincial Key Laboratory of Water Cycling and Eco–Geological Processes Xiamen 361021FujianChina China University of Geosciences(Beijing) Beijing 100083China Changsha Center of Natural Resources Comprehensive Survey China Geological SurveyChangsha 410600China Hydrogeological Environmental Geological Survey Center of China Geological Survey Tianjin 071501China China University of Geosciences Wuhan 430074China

The coastal areas of the lower reaches of Oujiang River Basin are rich in groundwater resources.However,the unsustainable exploitation and utilization of groundwater have led to significant changes in the groundwater environment.Understanding the characteristics and genesis of groundwater salinization is crucial for preventing its deterioration and ensuring sustainable utilization.In this study,a comprehensive approach combining the ion ratio method,mineral saturation index method and multivariate statistical analysis was employed to investigate the hydrochemical characteristics and main controlling factors in the study area.The findings reveal that:(1)Groundwater samples in study area exhibit a neutral to slightly alkaline pH.The predominant chemical types of unconfined water are HCO_(3)-Ca·Na,HCO_(3)·Cl-Na·Ca and HCO_(3)·SO_(4)-Ca·Na,while confined water mainly exhibits Cl·HCO_(3)-Na and Cl-Na types.(2)Salinity coefficients indicate an increase in salinity from unconfined to confined water.TDS,Na^(+)and Cl^(–)concentrations show an increasing trend from mountainous to coastal areas in unconfined water,while confined water displays variability in TDS,Na^(+)and Cl^(–)concentrations.(3)Groundwater salinity is mainly influenced by water-rock interactions,including the dissolution of halite and gypsum,cation exchange,and seawater intrusion etc.Additionally,human activities and carbonate dissolution contribute to salinity in unconfined water.Seawater intrusion is identified as the primary factor leading to higher salinity in confined water compared to unconfined water,with increasing cation exchange and seawater interaction observed from unconfined to confined water.

关键词： Hydrochemical multivariate statistical analysis Seawater intrusion

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Metabolomics-based comparative analysis of the effects of host and environment on Viscum coloratum metabolites and antioxidative activities

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Journal of Pharmaceutical analysis 2022年第2期12卷 243-252页

作者： Rui-Zhen Zhang Jing-Tao Zhao Wei-Qing Wang Rong-Hua Fan Rong Rong Zhi-Guo Yu Yun-Li Zhao Department of Pharmaceutical analysis School of PharmacyShenyang Pharmaceutical UniversityShenyang110016China School of Pharmacy University College London29-39 Brunswick SquareBloomsuryLondonWC1N 1AXUK Department of Sanitary Inspection School of Public HealthShenyang Medical CollegeShenyang110034China

Viscum coloratum(Kom.)Nakai is a well-known medicinal hemiparasite widely distributed in Asia.The synthesis and accumulation of its metabolites are affected by both environmental factors and the host plants,while the latter of which is usually overlooked.The purpose of this study was to comprehensively evaluate the effects of host and habitat on the metabolites in V.coloratum through multiple chemical and biological approaches.The metabolite profile of V.coloratum harvested from three different host plants in two habitats were determined by multiple chemical methods including high-performance liquid chromatography-ultraviolet(HPLC-UV),gas chromatography-flame ionization detector(GC-FID)and ultra-performance liquid chromatography quadrupole time of flight mass spectrometry(UPLC-QTOF/MS).The differences in antioxidant efficacy of V.coloratum were determined based on multiple in vitro models.The multivariate statistical analysis and data fusion strategy were applied to analyze the differences in metabolite profile and antioxidant activity of V.coloratum.Results indicated that the metabolite profile obtained by various chemical approaches was simultaneously affected by host and environment factors,and the environment plays a key role.Meanwhile,three main differential metabolites between two environment groups were identified.The results of antioxidant assay indicated that the environment has greater effects on the biological activity of V.coloratum than the host.Therefore,we conclude that the integration of various chemical and biological approaches combined with multivariate statistical and data fusion analysis,which can determine the influences of host plant and habitat on the metabolites,is a powerful strategy to control the quality of semi-parasitic herbal medicine.

关键词： Viscum coloratum Host Environment Plant metabolomics multivariate statistical analysis Biological activity

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Evaluation of hydro-chemistry in a phreatic aquifer in the Vindhyan Region, India, using entropy weighted approach and geochemical modelling

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Acta Geochimica 2023年第4期42卷 648-672页

作者： Ashutosh Mishra Aman Rai Prabuddh Kumar Mishra Suresh Chand Rai Department of Geography Delhi School of EconomicsUniversity of DelhiDelhi 110027India Department of Geography Shivaji CollegeUniversity of DelhiDelhi 110027India

Groundwater quality monitoring and geochemical characterization in the phreatic aquifer are critical for ensuring universal and equitable access to clean,reliable,and inexpensive drinking water for all.This research was intended to investigate the hydrogeochemical attributes and mechanisms regulating the chemistry of groundwater as well as to assess spatial variation in groundwater quality in Satna district,India.To accomplish this,the groundwater data comprising 13 physio-chemical parameters from thirty-eight phreatic aquifer locations were analysed for May 2020 by combining entropy-weighted water quality index(EWQI),multivariate statistics,geochemical modelling,and geographical information system.The findings revealed that the groundwater is fresh and slightly alkaline.Hardness was a significant concern as 57.89% of samples were beyond the permissible limit of the World Health Organisation.The dominance of ions were in the order of Ca^(2+)> Na^(+)> Mg^(2+)> K^(+) and HCO_(3)^(-)> SO_(4)^(2-)> Cl^-> NO_(3)^(-)> F^(-).Higher concentration of these ions is mainly concentrated in the northeast and eastern regions.Pearson correlation analysis and principal component analysis(PCA) demonstrated that both natural and human factors regulate groundwater chemistry in the region.The analysis of Q-mode agglomerative hierarchical clustering highlighted three significant water clusters.Ca-HCO_3 was the most prevalent hydro-chemical facies in all three clusters.Geochemical modelling through various conventional plots indicated that groundwater chemistry in the research region is influenced by the dissolution of calcite/dolomite,reverse ion exchange,and by silicate and halite weathering.EWQI data of the study area disclosed that 73.69% of the samples were appropriate for drinking.Due to high salinity,Magnesium(Mg^(2+)),Nitrate(NO_(3)^(-)),and Bicarbonate(HCO_(3)^(-)) concentrations,the north-central and north-eastern regions are particularly susceptible.The findings of the study may be accomplished by policymakers and groundwat

关键词： Groundwater quality assessment EWQI multivariate statistical analysis Geochemical modelling Hydrogeochemical processes Saturation index

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Metabolic regulation mechanism of Aconiti Radix Cocta extract in rats based on ^(1)H-NMR metabonomics

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Chinese Herbal Medicines 2022年第4期14卷 602-611页

作者： Wenfang Jin Jianli Bi Sheng Xu Mengfan Rao Qi Wang Yan Yuan Baolei Fan Department of Medicine Hubei University of Science and TechnologyXianning 437000China The First People’s Hospital of Tongshan County Xianning 437000China Hubei Engineering Research Center of Traditional Chinese Medicine of South Hubei Province Xianning 437000China

Objective:To establish a metabonomics research technique based on the combination of^(1)H-NMR and multivariate statistical analysis,so as to explore the metabolic regulation mechanism of Aconiti Radix Cocta extract(ARCE)in rat tissues and serum.Methods:SD rats were randomly divided into blank group,female group and male group.The^(1)H-NMR technique was used to collect the information of rat tissues and serum samples in each group.The principal component analysis(PCA),partial least squares discriminant analysis(PLS-DA)and other methods were used for data pattern recognition,so as to screen out potential differential metabolites and metabolic pathways,and then network analysis and KEGG database were used to analyze the relationship between metabolites,metabolic pathways and diseases.Results:The external features and^(1)H-NMR analysis showed that the sex of rats had no obvious effect on the drug action.A total of 15 potential differential metabolites and six metabolic pathways were screened out through data pattern recognition.Through network analysis and KEGG pathway analysis,three target diseases closely related to differential metabolites were found,and the metabolic pathway related to lung cancer was the central carbon metabolism of cancer.Conclusion:This study shows that Aconiti Radix Cocta(ARC)may regulate the energy metabolism of the body by influencing arginine synthesis,so as to play the roles of anti-inflammation,analgesia,anti-tumor and immune regulation.

关键词： Aconiti Radix Cocta ^(1)H-NMR metabolomics multivariate statistical analysis rats

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Spatio-temporal variations of water quality in Yuqiao Reservoir Basin, North China

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Frontiers of Environmental Science & Engineering 2015年第4期9卷 649-664页

作者： Yuan XU Ruqin XIE Yuqiu WANG Jian SHA College of Environmental Science and Engineering Nankai University Tianjin 300071 China

Fuzzy comprehensive assessment and multivariate statistical techniques including cluster analysis, discriminant analysis, principal component analysis, and factor analysis were applied to analyze the water quality status of Yuqiao Reservoir Basin, North China, for assessing its spatio-temporal variations and identifying potential pollution sources. In this paper, we considered data for 14 water quality parameters collected during 1990–2004 at 7 water quality monitoring sites. The results of fuzzy comprehensive assessment revealed that water quality in Yuqiao Reservoir Basin showed a downtrend from 1990 to 2001 with fluctuation, and a slowly upward trend after 2001. The major water quality belonged to Class III and IV. Besides, hierarchical cluster analysis divided 7 monitoring sites into two groups （Group A and B）, and 12 months into three periods （low-flow （LF）, normal-flow （NF）, and high-flow （HF） period）. Temp, pH, SS, T-har, DO, NO3-N and TP were identified as significant variables affecting spatial variations, and Temp, pH and NO2-N were identified as significant variables affecting temporal variations by discriminant analysis. Factor analysis identified four latent pollution sources for water quality variations： nutrient pollution, organic pollution, inorganic pollution, and natural pollution. Moreover, for Group A regions, pollution inputs mainly came from domestic wastewater and industrial sewage. For Group B regions, it is more likely that water pollution resulted from the combined effects of domestic wastewater, hospital wastewater, agriculture runoff, and fishpond discharge, as well as the incoming water from upstream.

关键词： Fuzzy comprehensive assessment multivariate statistical analysis water quality

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