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Network pharmacology approaches for research of Traditional Chinese Medicines

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Chinese Journal of Natural Medicines 2023年第5期21卷 323-332页

作者： LI Xiang LIU Ziqi LIAO Jie CHEN Qian LU Xiaoyan fan xiaohui School of Basic Medical Sciences and Forensic Medicine Hangzhou Medical CollegeHangzhou 311399China Department of Chinese Medicine Science&Engineering College of Pharmaceutical SciencesZhejiang UniversityHangzhou 310058China Innovation Center in Zhejiang University State Key Laboratory of Component-based Chinese MedicineHangzhou 310058China Future Health Laboratory Innovation Center of Yangtze River DeltaZhejiang UniversityJiaxing 314100China

Pharmacodynamics material basis and effective mechanisms are the two main issues to decipher the mechnisms of action of Traditional Chinese medicines(TCMs)for the treatment of diseases.TCMs,in“multi-component,multi-target,multi-pathway”paradigm,show satisfactory clinical results in complex diseases.New ideas and methods are urgently needed to explain the complex interactions between TCMs and diseases.Network pharmacology(NP)provides a novel paradigm to uncover and visualize the underlying interaction networks of TCMs against multifactorial diseases.The development and application of NP has promoted the safety,efficacy,and mechanism investigations of TCMs,which then reinforces the credibility and popularity of TCMs.The current organcentricity of medicine and the“one disease-one target-one drug”dogma obstruct the understanding of complex diseases and the development of effective drugs.Therefore,more attentions should be paid to shift from“phenotype and symptom”to“endotype and cause”in understanding and redefining current diseases.In the past two decades,with the advent of advanced and intelligent technologies(such as metabolomics,proteomics,transcriptomics,single-cell omics,and artificial intelligence),NP has been improved and deeply implemented,and presented its great value and potential as the next drug-discovery paradigm.NP is developed to cure causal mechanisms instead of treating symptoms.This review briefly summarizes the recent research progress on NP application in TCMs for efficacy research,mechanism elucidation,target prediction,safety evaluation,drug repurposing,and drug design.

关键词： Network Pharmacology Single-Cell omics Artificial Intelligence Traditional Chinese Medicine Herbal Medicine Pharmacodynamics Material Basis Effective Mechanism Drug Repurposing

Analysis of reflected signal of quad rotor UAV based on model fitting in mobile communication system

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Journal of Systems Engineering and Electronics 2022年第1期33卷 97-104页

作者： LI xiaohui fanG Cong fan Tao School of Telecommunication Engineering Xidian UniversityXi’an 710071China Guangzhou Institute of Technology Xidian UniversityGuangzhou 510555China

In view of the many scenes of unmanned aerial vehicle(UAV)detection,a third-party signal source is used to design a receiver to monitor the UAV.It is of great significance to understand the reflection of the signal illuminating the UAV.Taking the communication base station(BS)signal as the third-party signal source,and considering the complete transmission link,reflection changes and loss fading of the communication signal,this study conducts model fitting for irregular UAV targets,simplifying complex targets into a combination of simple targets.Furthermore,the influence of the dielectric constant of the target surface and the signal irradiation angle on the signal reflection is analyzed.The analysis shows that the simulation results of this model fitting method are consistent with the results of other literature,which provides theoretical support for the detection of low and slow small targets such as UAVs.

关键词： mobile communication signal quad rotor unmanned aerial vehicle(UAV) signal reflection model fitting

An ultra-robust fingerprinting method for quality assessment of traditional Chinese medicine using multiple reaction monitoring mass spectrometry

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Journal of Pharmaceutical Analysis 2021年第1期11卷 88-95页

作者： Zhenhao Li xiaohui Zhang Jie Liao xiaohui fan Yiyu Cheng Pharmaceutical Informatics Institute College of Pharmaceutical SciencesZhejiang UniversityHangzhou310058China

Chromatographic fingerprinting has been perceived as an essential tool for assessing quality and chemical equivalence of traditional Chinese medicine.However,this pattern-oriented approach still has some weak points in terms of chemical coverage and robustness.In this work,we proposed a multiple reaction monitoring(MRM)-based fingerprinting method in which approximately 100 constituents were simultaneously detected for quality assessment.The derivative MRM approach was employed to rapidly design MRM transitions independent of chemical standards,based on which the large-scale fingerprinting method was efficiently established.This approach was exemplified on QiShenYiQi Pill(QSYQ),a traditional Chinese medicine-derived drug product,and its robustness was systematically evaluated by four indices:clustering analysis by principal component analysis,similarity analysis by the congruence coefficient,the number of separated peaks,and the peak area proportion of separated peaks.Compared with conventional ultraviolet-based fingerprints,the MRM fingerprints provided not only better discriminatory capacity for the tested normal/abnormal QSYQ samples,but also higher robustness under different chromatographic conditions(i.e.,flow rate,apparent pH,column temperature,and column).The result also showed for such large-scale fingerprints including a large number of peaks,the angle cosine measure after min-max normalization was more suitable for setting a decision criterion than the unnormalized algorithm.This proof-of-concept application gives evidence that combining MRM technique with proper similarity analysis metrices can provide a highly sensitive,robust and comprehensive analytical approach for quality assessment of traditional Chinese medicine.

关键词： Multiple reaction monitoring Mass spectrometry-based fingerprinting Quality assessment Traditional Chinese medicine Robustness evaluation

Multimodal integrated strategy for the discovery and identification of quality markers in traditional Chinese medicine

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Journal of Pharmaceutical Analysis 2022年第5期12卷 701-710页

作者： Xiaoyan Lu Yanyan Jin Yuzhen Wang Yunlong Chen xiaohui fan Pharmaceutical Informatics Institute College of Pharmaceutical SciencesZhejiang UniversityHangzhou310058China Innovation Center in Zhejiang University State Key Laboratory of Component-Based Chinese MedicineHangzhou310058China Jinhua Institute of Zhejiang University JinhuaZhejiang321016China Westlake Laboratory of Life Sciences and Biomedicine Hangzhou310058China Hangzhou Children's Hospital Hangzhou310010China Department of Pharmacy Sir Run Run Shaw HospitalZhejiang University School of MedicineHangzhou310016China

With the modernization and internationalization of traditional Chinese medicine(TCM),the requirement for quality control has increased.The quality marker(Q-marker)is an important standard in this field and has been implemented with remarkable success in recent years.However,the establishment of Qmarkers remains fragmented and the process lacks systematicity,resulting in inconsistent quality control and insufficient correlation with clinical efficacy and safety of TCM.This review introduces four multimodal integrated approaches that contribute to the discovery of more comprehensive and accurate Qmarkers,thus aiding in the establishment of new quality control patterns based on the characteristics and principles of TCM.These include the whole-process quality control strategy,chemical-activity-based screening method,efficacy,safety,and consistent combination strategy,and TCM theory-guided approach.Furthermore,methodologies and representative examples of these strategies are described,and important future directions and questions in this field are also proposed.

关键词： Traditional Chinese medicine(TCM) Quality marker(Q-marker) Multimodal integrated strategy Quality control systems

Deep learning for fast channel estimation in millimeter-wave MIMO systems

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Journal of Systems Engineering and Electronics 2022年第6期33卷 1088-1095页

作者： LYU Siting LI xiaohui fan Tao LIU Jiawen SHI Mingli School of Telecommunication Engineering Xidian UniversityXi’an 710071China State Key Laboratory of Integrated Service Networks Xidian UniversityXi’an 710071China

Channel estimation has been considered as a key issue in the millimeter-wave(mmWave)massive multi-input multioutput(MIMO)communication systems,which becomes more challenging with a large number of antennas.In this paper,we propose a deep learning(DL)-based fast channel estimation method for mmWave massive MIMO systems.The proposed method can directly and effectively estimate channel state information(CSI)from received data without performing pilot signals estimate in advance,which simplifies the estimation process.Specifically,we develop a convolutional neural network(CNN)-based channel estimation network for the case of dimensional mismatch of input and output data,subsequently denoted as channel(H)neural network(HNN).It can quickly estimate the channel information by learning the inherent characteristics of the received data and the relationship between the received data and the channel,while the dimension of the received data is much smaller than the channel matrix.Simulation results show that the proposed HNN can gain better channel estimation accuracy compared with existing schemes.

关键词： millimeter-wave(mmWave) channel estimation deep learning(DL) dimensional mismatch channel state information(CSI)

Spatial pattern and driving factors of biomass carbon density for natural and planted coniferous forests in mountainous terrain,eastern Loess Plateau of China

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Forest Ecosystems 2020年第1期7卷 104-116页

作者： Lina Sun Mengben Wang xiaohui fan Institute of Loess Plateau Shanxi UniversityWucheng Road 92Taiyuan 030006China

Background:Understanding the spatial pattern and driving factors of forest carbon density in mountainous terrain is of great importance for monitoring forest carbon in support of sustainable forest management for mitigating climate change.Methods:We collected the forest inventory data in 2015 in Shanxi Province,eastern Loess Plateau of China,to explore the spatial pattern and driving factors of biomass carbon density(BCD)for natural and planted coniferous forests using Anselin Local Moran’s I,Local Getis-Ord G*and semivariogram analyses,and multi-group structural equation modeling,respectively.Results:The result of spatial pattern of BCDs for natural forests showed that the BCD was generally higher in the north but lower in the south of Shanxi.The spatial pattern for planted forests was substantially different from that for natural forests.The results of multi-group SEM suggested that elevation(or temperature as the alternative factor of elevation)and stand age were important driving factors of BCD for these two forest types.Compared with other factors,the effects of latitude and elevation on BCD showed much greater difference between these two forest types.The difference in indirect effect of latitude(mainly through affecting elevation and stand age)between natural and planted forests was to some extent a reflection of the difference between the spatial patterns of BCDs for natural and planted forests in Shanxi.Conclusions:The natural coniferous forests had a higher biomass carbon density,a stronger spatial dependency of biomass carbon density relative to planted coniferous forests in Shanxi.Elevation was the most important driving factor,and the effect on biomass carbon density was stronger for natural than planted coniferous forests.Besides,latitude presented only indirect effect on it for the two forest types.

关键词： Spatial pattern Spatial heterogeneity Multi-group structural equation modeling Stand age Elevation Mountainous terrain

Local features and manifold ranking coupled method for sketch-based 3D model retrieval

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Frontiers of Computer Science 2018年第5期12卷 1000-1012页

作者： xiaohui TAN Yachun fan Ruiliang GUO College of Information Engineering Capital Normal University Beijing 100048 China College of Information Science and Technology Beijing Normal University Beijing 100875 China School of Fashion Beijing Institute of Fashion Technology Beijing 100028 China

3D model retrieval virtual reality applications. In can benefit many downstream this paper, we propose a new sketch-based 3D model retrieval framework by coupling local features and manifold ranking. At technical fronts, we exploit spatial pyramids based local structures to facilitate the efficient construction of feature descriptors. Meanwhile, we propose an improved manifold ranking method, wherein all the categories between arbitrary model pairs will be taken into account. Since the smooth and detail-preserving line drawings of 3D model are important for sketch-based 3D model retrieval, the Difference of Gaussians （DOG） method is employed to extract the line drawings over the projected depth images of 3D model, and Bezier Curve is then adopted to further optimize the extracted line drawing. On that basis, we develop a 3D model retrieval engine to verify our method. We have conducted extensive experiments over various public benchmarks, and have made comprehensive comparisons with some state-of-the-art 3D retrieval methods. All the evaluation results based on the widely-used indicators prove the superiority of our method in accuracy, reliability, robustness, and versatility.

关键词： sketch-based retrieval 3D model manifoldranking line drawing local features

Changes in wind activity from 1957 to 2011 and their possible influence on aeolian desertification in northern China

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Journal of Arid Land 2015年第6期7卷 755-764页

作者： LI Jinchang LIU Haixia SU Zhizhu fan xiaohui State Key Laboratory of Earth Surface Processes and Resource Ecology Beijing Normal University Institute of Loess Plateau Shanxi University Historical Culture School Shanxi University

Wind activity is proved to have significant impacts on aeolian desertification. Clarifying the fluctuations and change trend of wind velocity is important for understanding their influence on aeolian desertification. In this study, we used a dataset of wind velocities collected from 93 meteorological stations across northern China from 1957 to 2011 to analyze the changes in wind activity during this period. We tested the monotonic and step（abrupt） trends for annual and seasonal data of mean wind velocity by using Mann-Kendall and Mann-Whitney tests, respectively. The results indicated that the annual mean wind velocity decreased by 0.83 m/s from 1957 to 2011. The decreasing trends were also significant（P〈0.01） for each season. The magnitude of the decrease was smallest in the east of northern China and largest in the west of northern China, and the most remarkable decrease occurred in the northwest of northern China. Abrupt decreases in annual and seasonal mean wind velocities occurred in the mid-1980 s, which was consistent with the changes in aeolian desertification since the mid-1980 s in northern China. As revealed by our study, although both modern aeolian desertification and ecosystem rehabilitation are affected by human activities to some extent, they are also likely to be strongly controlled by climate change, especially by wind activity.

关键词： wind velocity monotonic trend step trend aeolian desertification northern China

Modeling of spatial and temporal variations of ozone-NO_(x)-VOC sensitivity based on photochemical indicators in China

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Journal of Environmental Sciences 2022年第4期34卷 454-464页

作者： xiaohui Du Wei Tang Miaomiao Cheng Zhongzhi Zhang Yang Li Yu Li fan Meng State Key Laboratory of Environmental Criteria and Risk Assessment Chinese Research Academy of Environmental SciencesBeijing 100012China College of Water Sciences Beijing Normal UniversityBeijing 100857China Guangzhou Marine Geological Survey Guangzhou 510075China

Comprehensive air quality model with extensions(CAMx)-decoupled direct method(DDM)was used to simulate ozone-NO_(x)-VOCs sensitivity of for May-November in 2016-2018 in China.Based on the relationship between the simulated ozone(O_(3))sensitivity values and the ratio of formaldehyde(HCHO)to NO_(2)(FNR)and the ratio of production rate of hydrogen peroxide(H_(2)O_(2))to production rate of nitric acid(HNO_(3))(P_(H_(2)O_(2))/P_(HNO_(3))),the localized range of FNR and P_(H_(2)O_(2))/P_(HNO_(3))thresholds in different regions in China were obtained.The overall simulated FNR values are about 1.640-2.520,and P_(H_(2)O_(2))/P_(HNO_(3))values are about 0.540-0.830 for the transition regime.Model simulated O_(3)sensitivities or region specific FNR or P_(H_(2)O_(2))/P_(HNO_(3))thresholds should be applied to ensure the accurate local O3 sensitivity regimes.Using the tropospheric column FNR values from ozone monitoring instrument(OMI)satellite data as an indicator with the simulated threshold values,the spatial distributions of O_(3)formation regimes in China are determined.The O_(3)sensitivity regimes from eastern to central China are gradually from VOC-limited,transition to NO_(x)-limited spatially,and moving toward to transition or NO_(x)-limited regime from 2005 to 2019 temporally.

关键词： Ozone sensitivity analysis Photochemical indicator Ozone monitoring instrument(OMI) Formaldehyde NO_(2)