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Feedback on a shared big dataset for intelligent TBM PartⅠ:Feature extraction and machine learning methods

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Underground Space 2023年第4期11卷 1-25页

作者： Jian-Bin Li Zu-yu chen Xu Li Liu-Jie Jing yun-pei Zhangf Hao-Han Xiao Shuang-Jing Wang Wen-Kun Yang lei-Jie Wu Peng-yu Li Hai-Bo Li Min Yao Li-Tao Fan China Railway Group Co.Ltd. Beijing 100089China Department of geotechnical Engineering China Institute of Water Resources and Hydropower ResearchBeijing 100038China Key Laboratory of Urban Underground Engineering Ministry of EducationBeijing Jiaotong UniversityBeijing 100044China China Railway Engineering Equipment Group Co. Ltd.ZhengzhouHenan 450016China School of Civil Engineering Southeast UniversityNanjing 211189China Xi’an University of Technology Xi’an 710048China

This review summarizes the research outcomes and findings documented in 45 journal papers using a shared tunnel boring machine(TBM)dataset for performance prediction and boring efficiency optimization using machine learning *** big dataset was col-lected during the Yinsong water diversion project construction in China,covering the tunnel excavation of a 20 km-section with 199 items of monitoring metrics taken with an interval of one *** research papers were the result of a call for contributions during a TBM machine learning contest in 2019 and covered a variety of topics related to the intelligent construction of *** review com-prises two *** I is concerned with the data processing,feature extraction,and machine learning methods applied by the *** review finds that the data-driven and knowledge-driven approaches in extracting important features applied by various authors are diversified,requiring further studies to achieve commonly accepted *** techniques for cleaning and amending the raw data adopted by the contributors were summarized,indicating some highlights such as the importance of sufficiently high fre-quency of data acquisition(higher than 1 second),classification and standardization for the data preprocessing process,and the appro-priate selections of features in a boring *** review finds that both supervised and unsupervised machine learning methods have been utilized by various *** ensemble and deep learning methods have found wide *** I highlights the impor-tant features of the individual methods applied by the contributors,including the structures of the algorithm,selection of hyperparam-eters,and model validation approaches.

关键词： Big data Machine learning method TBM construction Data extraction Machine learning contest

Feedback on a shared big dataset for intelligent TBM Part Ⅱ:Application and forward look

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Underground Space 2023年第4期11卷 26-45页

作者： Jian-Bin Li Zu-yu chen Xu Li Liu-Jie Jing yun-pei Zhang Hao-Han Xiao Shuang-Jing Wang Wen-Kun Yang lei-Jie Wu Peng-yu Li Hai-Bo Li Min Yao Li-Tao Fan China Railway Group Co.Ltd Beijing 100089China Department of geotechnical Engineering China Institute of Water Resources and Hydropower ResearchBeijing 100038China Key Laboratory of Urban Underground Engineering Ministry of EducationBeijing Jiaotong UniversityBeijing 100044China China Railway Engineering Equipment Group Co. LtdZhengzhouHenan 450016China School of Civil Engineering Southeast UniversityNanjing 211189China Xi’an University of Technology Xi’an 710048China

This review discusses the application scenarios of the machine learning-supported performance prediction and the optimization effi-ciency of tunnel boring machines(TBMs).The rock mass quality ratings,which are based on the Chinese code for geological survey,were used to provide"labels"suitable for supervised *** a result,the generation of machine prediction for rock mass grades reason-ably agreed with the ground truth documented in geological *** contrast,the main operational parameters,i.e.,thrust and torque,can be reasonably predicted based on historical ***,18 collapse sections of the Yinsong project have been successfully predicted by several *** studies on the selection of the optimal penetration rate and cost were *** review also presents a summary of the main achievements in response to the initiatives of the Lotus Pool Contest in *** the first time,large and well-documented TBM performance data has been shared for joint scientific ***,the review discusses the technical problems that require further study and the perspectives in the future development of intelligent TBM construction based on big data and machine learning.

关键词： TBM performance prediction TBM rock mass quality rating TBM-supported machine learning Rock mass classification ensemble Tunnel collapse

Allotetraploidization event of Coptis chinensis shared by all Ranunculales

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Horticultural Plant Journal 2024年第1期10卷 288-303页

作者： Yan Zhang Weina ge Jia Teng Yanmei Yang Jianyu Wang Zijian yu Jiaqi Wang Qimeng Xiao Junxin zhao Shaoqi Shen Yishan Feng Shoutong Bao yu Li yuxian Li Tianyu lei yuxin Pan Lan Zhang Jinpeng Wang Department of Bioinformatics School of Life SciencesNorth China University of Science and TechnologyTangshanHebei 063000China School of Life Sciences North China University of Science and TechnologyTangshanHebei 063000China State Key Laboratory of Systematic and Evolutionary Botany Institute of BotanyChinese Academy of ScienceBeijing 100093China University of Chinese Academy of Sciences Beijing 100049China

Coptis chinensis Franch.,also named Chinese goldthread is a member of Ranunculaceae in the order Ranunculales and represents an important lineage of early eudicots with traditional medicinal *** our study,by using syntenic analysis combined with phylogenomic analysis of *** and four other representative genomes from basal and core eudicots,we confirmed that the WGD event in *** was shared by Aquilegia coerulea and Papaver somniferum *** quickly occurred after Ranunculales diverged from other eudicots,likely a Ranunculales common tetraploidization(RCT).The synonymous nucleotide substitutions at synonymous sites distribution of syntenic blocks across these genomes showed that the evolutionary rate of the *** genome is faster than that of the *** genome by approximately 13.7%,possibly due to Papaveraceaes having an additional special tetraploidization event(PST).After Ks correction,the RCT dated to 115—130 million years ago(MYA),which was close to the divergence of Ranunculaceaes and Papaveraceaes approximately115.45—130.51 ***,we identified homologous genes related to polyploidization and speciation and constructed multiple sequence alignments with different reference ***,the event-related subgenomes in the basal genomes all showed genomic fractionation bias,suggesting a likely allopolyploid nature of the RCT,PST and T-Alpha and T-Beta events in Tetracentron *** addition,we detected that the sixteen P450 subfamilies were markedly expanded in the genomes of Ranunculales,and most of them were related to the RCT and PST *** constructed a new platform for Early Eudicot Comparative genomic Research(http://***/***)to store more *** summary,our findings support the WGD of *** shared by Ranunculales,which is likely an allotetraploidization *** present effort offered new insights into the evolution of key polyploidization events and the genes related to second

关键词： Coptis chinensis Ranunculales Polyploidization genomic fractionation P450 genes

Semitransparent organic photovoltaics enabled by transparent p-type inorganic semiconductor and near-infrared acceptor

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Journal of Energy Chemistry 2024年第9期96卷 351-358页

作者： Xue Yan Jiayu Wang Wei He Top Archie Dela Peña Can Zhu Hailin yu Yingyue Hu Cenqi Yan Shengqiang Ren Xingyu chen Zhe Wang Jiaying Wu Mingjie Li Jianlong Xia lei Meng Shirong Lu Dewei zhao Mikhail Artemyev Yongfang Li pei cheng College of Polymer Science and Engineering State Key Laboratory of Polymer Materials EngineeringSichuan UniversityChengdu 610065SichuanChina Department of Applied Physics The Hong Kong Polytechnic UniversityKowloonHong Kong 999077China Beijing National Laboratory for Molecular Sciences CAS Key Laboratory of Organic SolidsInstitute of ChemistryChinese Academy of SciencesBeijing 100190China College of Materials Science and Engineering&Engineering Research Center of Alternative Energy Materials&Devices Ministry of EducationSichuan UniversityChengdu 610065SichuanChina Department of Material Science and Technology Taizhou UniversityTaizhou 318000ZhejiangChina Advanced Materials Thrust Function HubThe Hong Kong University of Science and Technology(Guangzhou)Guangzhou 511400GuangdongChina State Key Laboratory of Advanced Technology for Materials Science and Processing Center of Smart Materials and DevicesWuhan University of TechnologyWuhan 430070HubeiChina Department of Civil1nd Environmental Engineering The Hong Kong University of Science and TechnologyHong Kong 999077China Research Institute for Physical Chemical Problems Belarusian State UniversityMinsk 220006Belarus

Semitransparent organic photovoltaics(STOPVs)have gained wide attention owing to their promising applications in building-integrated photovoltaics,agrivoltaics,and floating *** semiconductors with high charge carrier mobility usually have planar and conjugated structures,thereby showing strong absorption in visible *** this work,a new concept of incorporating transparent inorganic semiconductors is proposed for high-performance ***(I)thiocyanate(CuSCN)is a visible-transparent inorganic semiconductor with an ionization potential of 5.45 eV and high hole *** transparency of CuSCN benefits high average visible transmittance(AVT)of *** energy levels of CuSCN as donor match those of near-infrared small molecule acceptor BTP-eC9,and the formed heterojunction exhibits an ability of exciton *** mobility of CuSCN contributes to a more favorable charge transport channel and suppresses charge *** control STOPVs based on PM6/BTP-eC9 exhibit an AVT of 19.0%with a power conversion efficiency(PCE)of 12.7%.Partial replacement of PM6 with CuSCN leads to a 63%increase in transmittance,resulting in a higher AVT of 30.9%and a comparable PCE of 10.8%.

关键词： Copper(I)thiocyanate Inorganic semiconductor Semitransparent Organic photovoltaics Charge dissociation

COSINE:A web server for clonal and subclonal structure inference and evolution in cancer genomics

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Zoological Research 2022年第1期43卷 75-77页

作者： Xi-Guo yuan yuan zhao Yang Guo Lin-Mei ge Wei Liu Shi-yu Wen Qi Li Zhang-Bo Wan pei-Na Zheng Tao Guo Zhi-Da Li Martin peifer yu-Peng Cun School of Computer Science and Technology Xidian UniversityXi'anShaanxi 710071China iFlora Bioinformatics Center Germplasm Bank of Wild SpeciesKunming Institute of BotanyChinese Academy of SciencesKunmingYunan 650201China yuxi Rongjian Information Technology Co. Ltd.YuxiYunan 653100China Center for Molecular Medicine Cologne(CMMC) University of CologneCologne 50931Germany Pediatric Research Institute Ministry of Education Key Laboratory of Child Development and DisordersNational Clinical Research Center for Child Health and DisordersChina International Science and Technology Cooperation Base of Child Development and Critical DisordersChongqing Key Laboratory of Translational Medical Research in Cognitive Development and Learning and Memory DisordersChildren’s Hospital of Chongqing Medical UniversityChongqing 400014China

Cancer cell genomes originate from single-cell mutation with sequential clonal and subclonal expansion of somatic mutation acquisition during pathogenesis,thus exhibiting a Darwinian evolutionary process(gerstung et al.,2020;Nik-Zainal et al.,2012).Through next-generation sequencing of tumor tissue,this evolutionary process can be characterized by statistical modelling,which can identify the clonal state,somatic mutation order,and evolutionary process(gerstung et al.,2020;Mcgranahan&Swanton,2017).Inference of clonal and subclonal structure from bulk or single-cell tumor genomic sequencing data has a huge impact on studying cancer *** state and mutation order can provide detailed insight into tumor origin and future *** the past decade,various methods for subclonal reconstruction using bulk tumor sequencing data have been ***,these methods had different programming languages and data input formats,which limited their use and ***,we established a web server for Clonal and Subclonal Structure Inference and Evolution(COSINE)of cancer genomic data,which incorporated twelve popular subclonal reconstruction *** deconstructed each method to provide a detailed workflow of single processing steps with a user-friendly *** the best of our knowledge,this is the first web server providing online subclonal inference based on the integration of most popular subclonal reconstruction *** is freely accessible at ***.

关键词： .net server COSINE

Virus load and virus shedding of SARS-CoV-2 and their impact onpatient outcomes

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World Journal of Clinical Cases 2020年第24期8卷 6252-6263页

作者： pei-Fen chen Xia-Xia yu Yi-Peng Liu Di Ren Min Shen Bing-Sheng Huang Jun-Ling Gao heng-Yang Huang Ming Wu Wei-Yan Wang Li chen Xia Shi zhao-Qing Wang Ying-Xia Liu lei Liu Yong Liu Department of Respiratory Diseases Shenzhen Key Laboratory of Pathogen and ImmunityNational Clinical Research Center for Infectious DiseaseState Key Discipline of Infectious DiseasesShenzhen Third People’s HospitalThe Second Hospital Affiliated to Southern University of Science and TechnologyShenzhen 518114Guangdong ProvinceChina School of Biomedical Engineering Health Science CenterShenzhen UniversityShenzhen 518060Guangdong ProvinceChina Expert Panel of Shenzhen 2019-nCoV Pneumonia The Second People’s Hospital of ShenzhenShenzhen 518035Guangdong ProvinceChina Shenzhen Key Laboratory of Pathogen and Immunity National Clinical Research Center for Infectious DiseaseState Key Discipline of Infectious DiseasesShenzhen Third People’s HospitalThe Second Hospital Affiliated to Southern University of Science and TechnologyShenzhen 518114Guangdong ProvinceChina Medical AI Laboratory School of Biomedical EngineeringHealth Science CentreShenzhen UniversityShenzhen 518060Guangdong ProvinceChina Buddhism and Science Research Laboratory Centre of Buddhist StudiesThe University of Hong KongPokfulamHong Kong 999077China ICU The Second People's Hospital of ShenzhenShenzhen 518035Guangdong ProvinceChina Expert Panel of Shenzhen 2019-nCoV Pneumonia Shenzhen HospitalSouthern Medical UniversityShenzhen 518000Guangdong ProvinceChina

BACKGROUND Understanding a virus shedding patterns in body fluids/secretions is importantto determine the samples to be used for diagnosis and to formulate infectioncontrol *** To investigate the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)shedding patterns and its risk *** All laboratory-confirmed coronavirus disease 2019 patients with completemedical records admitted to the Shenzhen Third People’s Hospital from January28, 2020 to March 8, 2020 were included. Among 145 patients (54.5% males;median age, 46.1 years), three (2.1%) died. The bronco-alveolar lavage fluid(BALF) had the highest virus load compared with the other samples. The viralload peaked at admission (3.3 × 108 copies) and sharply decreased 10 d *** The viral load was associated with prolonged intensive care unit (ICU) *** in the ICU had significantly longer shedding time compared to those inthe wards (P ge > 60 years [hazard ratio (HR) = 0.6;95% confidenceinterval (CI): 0.4-0.9] was an independent risk factor for SARS-CoV-2 shedding,while chloroquine (HR = 22.8;95%CI: 2.3-224.6) was a protective *** BALF had the highest SARS-CoV-2 load. Elderly patients had higher virus loads,which was associated with a prolonged ICU stay. Chloroquine was associatedwith shorter shedding duration and increased the chance of viral negativity.

关键词： COVID-19 Virus shedding Viral load Patient outcome China Infectious disease

Mechanoresponsive MiR-138-5p Targets MACF1 to Inhibit Bone Formation

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医用生物力学 2019年第A1期34卷 72-73页

作者： Zhihao chen zhao Fan Liang Chao Lifang Hu chen lei Zhang Yan Yin Chong Dijie Li Tian Ye Wuxia Qiu Kewen Zhang Chaofei Yang Xiaona Li Li yu Weiyi chen Zhang ge Qian Airong Lab for Bone Metabolism Key Lab for Space Biosciences and BiotechnologyResearch Center for Special Medicine and Health Systems EngineeringNPU-UAB Joint Laboratory for Bone MetabolismSchool of Life SciencesNorthwestern Polytechnical UniversityXi’an710072China Northwestern Polytechnical University-Hong Kong Baptist UniversityJoint Rese arch Centre for Translational Medicine on Musculoskeletal Health in Space Xi’an710072China Institute forAdvancing Translational Medicine in Bone and Joint Diseases School of Chinese MedicineHong Kong Baptist UniversityHong Kong College of Biomedical Engineering Taiyuan University of TechnologyTaiyuan030024China

Mechanical stimuli play an essential role in maintaining bone remodeling and skeletal ***,bone can respond to the changes of mechanical condition to adjust its mass and *** studies discover that bedridden patients showed osteoporotic T-scores and low bone mineral density,and long-term immobilized patients presented reduced markers of bone ***,as bone formation mediated by osteoblast differentiation is a complex process,the underlying molecular mechanism of mechanical stimuli regulating bone formation is still *** evidences show that microRNAs(miRNAs)are involved in mechanical stimuli regulating bone formation or osteoblast ***,no direct evidence identifies mechanoresponsive miRNA in both human and animal bones,and clarifies its mechanoresponsive role under different mechanical conditions(*** unloading,reloading,loading).In the current study,we screened for differentially expressed miRNAs in bone specimens of bedridden patients with fractures,then identified that the expression of miR-138-5p,but not the other miRNAs,altered withbedridden time and was negatively correlated with the expression of the bone formation marker genes Alp(alkaline phosphatase).Moreover,miR-138-5p was up-regulated with reduced bone formation during unloading and down-regulated with increased bone formation during reloading in hind4imb unloaded *** addition,miR-138-5p was verified to be responsive to different mechanical unloading condition and cyclic mechanical stretch condition in primary osteogenic cells,*** in vitro data suggested that mechanoresponsive miR-138-5p directly targeted microtubule actin crosslinking factor 1(MACF1)to inhibit osteoblast *** vivo,we constructed an osteoblastic miR-138-5p transgenic mice model(TG138)with the Runx2promoter,and found that overexpression miR-138-5p supressed bone ***,osteoblast-targeted inhibition of miR-13

关键词： Mechanoresponse miR-138-5p MACF1 bone formation

Effects of viral infection and microbial diversity on patients with sepsis:A retrospective study based on metagenomic next-generation sequencing

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World Journal of Emergency Medicine 2021年第1期12卷 29-35页

作者： Li-wei Duan Jin-long Qu Jian Wan Yong-hua Xu Yi Shan Li-xue Wu Jin-hao Zheng Wei-wei Jiang Qi-tong chen Yan Zhu Jian Zhou Wen-bo yu lei pei Xi Song Wen-fang Li zhao-fen Lin Department of Emergency and Critical Care Medicine Changzheng Hospitalthe Second Military Medical UniversityShanghai 200003China Department of Emergency and Critical Care Medicine Pudong New Area People’s HospitalShanghai 201299China

BACKGROUND: The study aims to investigate the performance of a metagenomic next-generationsequencing (NGS)-based diagnostic technique for the identifi cation of potential bacterial and viral infectionsand eff ects of concomitant viral infection on the survival rate of intensive care unit (ICU) sepsis ***: A total of 74 ICU patients with sepsis who were admitted to our institution from February1, 2018 to June 30, 2019 were enrolled. Separate blood samples were collected from patients for bloodcultures and metagenomic NGS when the patients’ body temperature was higher than 38 °C. Patients’demographic data, including gender, age, ICU duration, ICU scores, and laboratory results, were *** correlations between pathogen types and sepsis severity and survival rate were ***: NGS produced higher positive results (105 of 118;88.98%) than blood cultures(18 of 118;15.25%) over the whole study period. Concomitant viral infection correlated closelywith sepsis severity and had the negative effect on the survival of patients with sepsis. However,correlation analysis indicated that the bacterial variety did not correlate with the severity of ***: Concurrent viral load correlates closely with the severity of sepsis and thesurvival rate of the ICU sepsis patients. This suggests that prophylactic administration of antiviraldrugs combined with antibiotics may be benefi cial to ICU sepsis patients.

关键词： Sepsis Metagenomic next-generation sequencing Viral infections Bacterial infections Microbial diversity

METTL14 is a chromatin regulator independent of its RNA N^(6)-methyladenosine methyltransferase activity

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Protein & Cell 2023年第9期14卷 683-697页

作者： Xiaoyang Dou Lulu Huang yu Xiao Chang Liu Yini Li Xinning Zhang Lishan yu Ran zhao lei Yang Chuan chen Xianbin yu Boyang Gao Meijie Qi Yawei Gao Bin Shen Shuying Sun Chuan He Jun Liu Department of Chemistry and Institute for Biophysical Dynamics University of ChicagoChicagoIL 60637USA Howard Hughes Medical Institute ChicagoIL 60637USA State Key Laboratory of Protein and Plant gene Research Peking-Tsinghua Center for Life SciencesSchool of Life SciencesPeking UniversityBeijing 100871China Department of Physiology and Brain Science Institute Johns Hopkins University School of MedicineBaltimoreMD 21205USA Institute for Regenerative Medicine Shanghai East HospitalShanghai Key Laboratory of Signaling and Disease ResearchFrontier Science Center for Stem Cell ResearchSchool of Life Sciences and TechnologyTongji UniversityShanghai 200120China The Institute of Translational Medicine School of MedicineZhejiang UniversityHangzhou 310029China Division of Life Sciences and Medicine Center for Reproductive MedicineThe First Affiliated Hospital of USTCUniversity of Science and Technology of ChinaHefei230000China Clinical and Translational Research Center of Shanghai First Maternity&Infant Hospital Shanghai Key Laboratory of Signaling and Disease ResearchFrontier Science Center for Stem Cell ResearchSchool of Life Sciences and TechnologyTongji UniversityShanghai 200092China State Key Laboratory of Reproductive Medicine Center for Global HealthGusu SchoolWomen's Hospital of Nanjing Medical UniversityNanjing Maternity and Child Health Care HospitalNanjing Medical UniversityNanjing211166China Department of Biochemistry and Molecular Biology University of ChicagoChicagoIL 60637USA

METTL3 and METTL14 are two components that form the core heterodimer of the main RNA m^(6)A methyltransferase complex(MTC)that installs m^(6)***,depletion of METTL3 or METTL14 displayed distinct effects on stemness maintenance of mouse embryonic stem cell(mESC).While comparable global hypo-methylation in RNA m^(6)A was observed in Mettl3 or Mettl14 knockout mESCs,***14 knockout led to a globally decreased nascent RNA synthesis,whereas Mettl3 depletion resulted in transcription upregulation,suggesting that METTL14 might possess an mA-independent role in gene *** found that METTL14 colocalizes with the repressive H3K27me3 ***,METTL14,but not METTL3,binds H3K27me3 and recruits KDM6B to induce H3K27me3 demethylation independent of *** of METTL14 thus led to a global increase in H3K27me3 level along with a global gene *** effects of METTL14 on regulation of H3K27me3 is essential for the transition from self-renewal to differentiation of *** work reveals a regulatory mechanism on heterochromatin by METTL14 in a manner distinct from METTL3 and independently of m^(6)A,and critically impacts transcriptional regulation,stemness maintenance,and differentiation ofmESCs.

关键词： METTL14 chromatin H3K27me3 m^(6)A-independent mESC differentiation