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Knowledge Graph Enhanced Transformers for Diagnosis Generation of Chinese Medicine

Chinese Journal of Integrative Medicine 2024年第3期30卷 267-276页

作者： WANG Xin-yu YANG Tao GAO Xiao-yuan hu Kong-fa School of Artificial Intelligence and Information Technology Nanjing University of Chinese MedicineNanjing210023China School of Information Management Nanjing UniversityNanjing210023China Jiangsu Collaborative Innovation Center of Traditional Chinese Medicine in Prevention and Treatment of Tumor Nanjing210023China Jiangsu Province Engineering Research Center of TCM Intelligence Health Service Nanjing210023China

Chinese medicine(CM)diagnosis intellectualization is one of the hotspots in the research of CM modernization.The traditional CM intelligent diagnosis models transform the CM diagnosis issues into classification issues,however,it is difficult to solve the problems such as excessive or similar categories.With the development of natural language processing techniques,text generation technique has become increasingly mature.In this study,we aimed to establish the CM diagnosis generation model by transforming the CM diagnosis issues into text generation issues.The semantic context characteristic learning capacity was enhanced referring to Bidirectional Long Short-Term Memory(BILSTM)with Transformer as the backbone network.Meanwhile,the CM diagnosis generation model Knowledge Graph Enhanced Transformer(KGET)was established by introducing the knowledge in medical field to enhance the inferential capability.The KGET model was established based on 566 CM case texts,and was compared with the classic text generation models including Long Short-Term Memory sequence-to-sequence(LSTM-seq2seq),Bidirectional and Auto-Regression Transformer(BART),and Chinese Pre-trained Unbalanced Transformer(CPT),so as to analyze the model manifestations.Finally,the ablation experiments were performed to explore the influence of the optimized part on the KGET model.The results of Bilingual Evaluation Understudy(BLEU),Recall-Oriented Understudy for Gisting Evaluation 1(ROUGE1),ROUGE2 and Edit distance of KGET model were 45.85,73.93,54.59 and 7.12,respectively in this study.Compared with LSTM-seq2seq,BART and CPT models,the KGET model was higher in BLEU,ROUGE1 and ROUGE2 by 6.00–17.09,1.65–9.39 and 0.51–17.62,respectively,and lower in Edit distance by 0.47–3.21.The ablation experiment results revealed that introduction of BILSTM model and prior knowledge could significantly increase the model performance.Additionally,the manual assessment indicated that the CM diagnosis results of the KGET model used in this study were highly consistent with the p

关键词： Chinese medicine diagnosis knowledge graph enhanced transformer text generation

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Washed microbiota transplantation for Crohn’s disease:A metagenomic,metatranscriptomic,and metabolomic-based study

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World Journal of Gastroenterology 2024年第11期30卷 1572-1587页

作者： Shi-Ju Chen Da-Ya Zhang Xia Wu fa-Ming Zhang Bo-Ta Cui Yi-Hao huang Zu-Lun Zhang rui Wang Fei-hu Bai Graduate School Hainan Medical UniversityHaikou 571199Hainan ProvinceChina Department of Microbiota Medicine&Medical Center for Digestive Diseases The Second Affiliated Hospital of Nanjing Medical UniversityNanjing 210011Jiangsu ProvinceChina Department of Gastroenterology The Second Affiliated Hospital of Hainan Medical UniversityHaikou 570216Hainan ProvinceChina

BACKGROUND Fecal microbiota transplantation(FMT)is a promising therapeutic approach for treating Crohn’s disease(CD).The new method of FMT,based on the automatic washing process,was named as washed microbiota transplantation(WMT).Most existing studies have focused on observing the clinical phenomena.However,the mechanism of action of FMT for the effective management of CD-particularly in-depth multi-omics analysis involving the metagenome,metatranscriptome,and metabolome-has not yet been reported.AIM To assess the efficacy of WMT for CD and explore alterations in the microbiome and metabolome in response to WMT.METHODS We conducted a prospective,open-label,single-center clinical study.Eleven CD patients underwent WMT.Their clinical responses(defined as a decrease in their CD Activity Index score of>100 points)and their microbiome(metagenome,metatranscriptome)and metabolome profiles were evaluated three months after the procedure.RESULTS Seven of the 11 patients(63.6%)showed an optimal clinical response three months post-WMT.Gut microbiome diversity significantly increased after WMT,consistent with improved clinical symptoms.Comparison of the metagenome and metatranscriptome analyses revealed consistent alterations in certain strains,such as faecalibac-terium prausnitzii,Roseburia intestinalis,and Escherichia coli.In addition,metabolomics analyses demonstrated that CD patients had elevated levels of various amino acids before treatment compared to the donors.However,levels of vital amino acids that may be associated with disease progression(e.g.,L-glutamic acid,gamma-glutamyl-leucine,and prolyl-glutamine)were reduced after WMT.CONCLUSION WMT demonstrated therapeutic efficacy in CD treatment,likely due to the effective reconstruction of the patient’s microbiome.Multi-omics techniques can effectively help decipher the potential mechanisms of WMT in treating CD.

关键词： Crohn’s disease Clinical trials Fecal microbiota transplant Metagenome Metatranscriptome Metabolome

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Removal of pathogenic indicator microorganisms during partial nitrification:the role of free nitrous acid

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Frontiers of Environmental Science & Engineering 2024年第3期18卷 93-102页

作者： Jiaojiao Xu Xiaotian Chen rui Tang Jingwei Feng Shoujun Yuan Wei Wang Zhen-hu hu Anhui Engineering Laboratory of Rural Water Environment and Resource School of Civil EngineeringHefei University of TechnologyHefei 230009China Hefei 168 High School Hefei 230025China Shanghai Key Laboratory of Materials Protection and Advanced Materials in Electric Power Shanghai University of Electric PowerShanghai 200090China

Digested wastewater contains pathogenic microorganisms and high ammonia concentrations,which can pose a potential risk to public health.Effective removal of pathogens and nitrogen is crucial for the post-treatment of digested wastewater.Partial nitrification-anammox is an energy-saving nitrogen removal process.Free nitrous acid(FNA),an intermediate product of partial nitrification,has the potential to inactivate microorganisms.However,the efficiency and mechanisms of FNA-related inactivation in pathogens during partial nitrification remains unclear.In this study,Enterococcus and Escherichia coli(E.coli)were selected to investigate the efficiency and mechanisms of FNA-related inactivation in partial nitrification process.The results revealed that 83%±13%and 59%±27%of E.coli and Enterococcus were removed,respectively,in partial nitrification process at FNA concentrations of 0.023−0.028 mg/L.When the concentration of FNA increased from 0 to 0.5 mg/L,the inactivation efficiencies of E.coli and Enterococcus increased from 0 to 99.9%and 89.9%,respectively.Enterococcus exhibited a higher resistance to FNA attack compared to E.coli.3D-laser scanning microscopy(3D-LSM)and scanning electron microscopy(SEM)revealed that FNA exposure caused the surface collapse of E.coli and Enterococcus,as well as visible pore formation on the surface of E.coli cells.4',6-Diamidino-2-phenylindole dihydrochloride n-hydrate(DAPI)/propidium iodide(PI)and biomolecule leakage confirmed that inactivation of E.coli and Enterococcus occurred due to breakdown of cell walls and cell membranes.These findings indicate that partial nitrification process can be used for the removal of residual pathogenic microorganisms.

关键词： Partial nitrification Free nitrous acid Pathogenic indicator microorganism Inactivation Cell structure

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Learning background restoration and local sparse dictionary for infrared small target detection

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Optoelectronics Letters 2024年第7期20卷 437-448页

作者： HE Yue ZHANG rui XI Chunmei Zhu hu School of Communications and Information Engineering Nanjing University of Posts and Telecommunications

This paper proposes a method for learning background restoration for infrared small target detection, employing a local sparse dictionary alongside an equalized structural texture representation. The method is specifically designed for the detection of small infrared targets, accommodating various levels of brightness, spatial size, and intensity. Our proposed model intelligently combines global low-rankness and local sparsity to estimate the rank of the background tensor, leveraging spatial and structural information to overcome the limitations posed by insufficient detailed texture knowledge. Subsequently, a structural texture representation, combining local gradient maps and local intensity maps, is applied to emphasize small objects. By comparing our method with nine advanced and representative approaches and quantifying the comparison using various metrics, the experimental results indicate that our proposed method has achieved favorable outcomes in both quantitative assessments and visual results.

关键词： A

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Burning Numbers of Barbells

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Acta Mathematicae Applicatae Sinica 2024年第2期40卷 526-538页

作者： hui-qing LIU rui-ting ZHANG Xiao-lan hu hubei Key Laboratory of Applied Mathematics&faculty of Mathematics and Statistic Hubei UniversityWuhan 430062China hubei Key Laboratory of Mathematical Sciences&School of Mathematics and Statistics Central China Normal UniversityWuhan 430079China

Motivated by a discrete-time process intended to measure the speed of the spread of contagion in a graph,the burning number b(G)of a graph G,is defined as the smallest integer k for which there are vertices x1,…xk su... 详细信息

关键词： burning number short/long barbell isometric subtree cycle

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Building mm Wave on the Evolving C-V2X:mm Wave NR-V2X

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China Communications 2024年第1期21卷 88-101页

作者： Shanzhi Chen Xinxin He rui Zhao Jinling hu Xin Zhang China Information and Communication Technology Group Co. Ltd.(CICT)the State Key Laboratory of Wireless Mobile CommunicationsBeijing 100083China Beijing Laboratory of Advanced Information Networks Beijing Key Laboratory of Network System Architecture and ConvergenceBeijing University of Posts and TelecommunicationsBeijing 100876China CICT Connected and Intelligent Technologies Co. LtdChina Academy of Telecommunication TechnologyBeijing 100191China CICT Mobile Communications Technology Co.Ltd.

Since the evolving standardization of cellular V2X(C-V2X)technologies is continuously developed by 3GPP,research on new radio(NR-V2X)has been on schedule by academic and industries.Though millimeter wave(mm Wave)frequency band is supposed to provide large transmission bandwidth,yet the development of mm Wave band in NR-V2X is still in preliminary stage.In this article,a comprehensive discussion of mm Wave NR-V2X is given covering trends,standardization landscape,and enabling technologies,aiming at tackling the challenge of channel modeling,directional channel access,beamforming and blockage management.The vision of mm Wave NR-V2X is to fully support the development of automated driving,holographic control display and improved in-car infotainment for the future.

关键词： C-V2X enabling technologies mmWave NR-V2X

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A Weakly-Supervised Crowd Density Estimation Method Based on Two-Stage Linear Feature Calibration

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IEEE/CAA Journal of Automatica Sinica 2024年第4期11卷 965-981页

作者： Yong-Chao Li rui-Sheng Jia Ying-Xiang hu Hong-Mei Sun the College of Computer Science and Engineering Shandong University of Science and TechnologyQingdao 266590 the faculty of Information Science and Engineering Ocean University of ChinaQingdao 266000China the College of Computer Science and Engineering Shandong University of Science and TechnologyQingdao 266590China the College of Computer Science and Engineering Nanjing University of Science and TechnologyNanjing 210000China

In a crowd density estimation dataset,the annotation of crowd locations is an extremely laborious task,and they are not taken into the evaluation metrics.In this paper,we aim to reduce the annotation cost of crowd datasets,and propose a crowd density estimation method based on weakly-supervised learning,in the absence of crowd position supervision information,which directly reduces the number of crowds by using the number of pedestrians in the image as the supervised information.For this purpose,we design a new training method,which exploits the correlation between global and local image features by incremental learning to train the network.Specifically,we design a parent-child network(PC-Net)focusing on the global and local image respectively,and propose a linear feature calibration structure to train the PC-Net simultaneously,and the child network learns feature transfer factors and feature bias weights,and uses the transfer factors and bias weights to linearly feature calibrate the features extracted from the Parent network,to improve the convergence of the network by using local features hidden in the crowd images.In addition,we use the pyramid vision transformer as the backbone of the PC-Net to extract crowd features at different levels,and design a global-local feature loss function(L2).We combine it with a crowd counting loss(LC)to enhance the sensitivity of the network to crowd features during the training process,which effectively improves the accuracy of crowd density estimation.The experimental results show that the PC-Net significantly reduces the gap between fullysupervised and weakly-supervised crowd density estimation,and outperforms the comparison methods on five datasets of Shanghai Tech Part A,ShanghaiTech Part B,UCF_CC_50,UCF_QNRF and Jhu-CROWD++.

关键词： Crowd density estimation linear feature calibration vision transformer weakly-supervision learning

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Simultaneously enhanced electrochemical performance and air stability of Ni-rich cathode with a modified washing process

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Rare Metals 2024年第1期43卷 87-97页

作者： Ben-rui hu Ying-Yi Yuan Yu-Cheng Wang Xun-hui Xiong School of Environment and Energy Guangdong Provincial Key Laboratory of Advanced Energy Storage MaterialsSouth China University of TechnologyGuangzhou 510640China

Water washing has been regarded as one of the most effective strategies to remove surface residual lithium of nickel-rich layered oxides for lithium-ion batteries(LIBs).However,the loss of lattice lithium during the water washing process deteriorates the electrochemical performances and air stability.Herein,washing the LiNi_(0.90)Co_(0.05)Al_(0.02)O_(2)(NCA) with ammonium dihydrogen phosphate(NH_(4)H_(2)PO_(4)) solution has been proposed to simultaneously enhance electrochemical performances and air stability,in which in-situ generated Li_(3)PO_(4) coating layer on surface of NCA can suppress the loss of lattice lithium.Besides,as a fast ionic conductor,Li_(3)PO_(4) coating layer on NCA can prevent the direct contact with electrolyte/air.As a result,the NH_(4)H_(2)PO_(4) solution washed NCA cathode can deliver a high capacity of131.9 mAh·g^(-1) at 10.0C rate as well as impressive cycle stability with a capacity retention of 83.1% after 100 cycles at 1.0C,much higher than those of water washed NCA(WS-NCA) electrode.After exposed in air for 7 days,the NH_(4)H_(2)PO_(4) solution washed NCA electrode can more effectively maintain the structural integrity as well as the electrochemical performances than water-washed NCA.This work provides a simple and effective approach to enhance the cycle stability and air stability of Nickel-rich cathode materials.

关键词： Layered Ni-rich cathode Residual lithium Li_(3)PO_(4)coating Rate performance Air stability

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HSP110 aggravates ischemia-reperfusion injury after liver transplantation by promoting NF-κB pathway

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Hepatobiliary & Pancreatic Diseases International 2024年第4期23卷 344-352页

作者： Qing-Zhi hu Zhen-rui Cao Wei-Xiong Zheng Min-Jie Zhao Jun-hua Gong Cong Chen Zhong-Jun Wu rui Tao Department of Hepatobiliary Surgery Bishan Hospital of Chongqing Medical UniversityChongqing 402760China Department of Cardiothoracic Surgery the First Affiliated Hospital of Chongqing Medical UniversityChongqing 400016China c Department of Hepatobiliary Surgery the First Affiliated Hospital of Chongqing Medical UniversityChongqing 400016China Department of Hepatobiliary Surgery the Second Affiliated Hospital of Chongqing Medical UniversityChongqing 400010China

Background:Ischemia-reperfusion injury(IRI)poses a significant challenge to liver transplantation(LT).The underlying mechanism primarily involves overactivation of the immune system.Heat shock protein 110(HSP110)functions as a molecular chaperone that helps stabilize protein structures.Methods:An IRI model was established by performing LT on Sprague-Dawley rats,and HSP110 was silenced using siRNA.Hematoxylin-eosin staining,TUNEL,immunohistochemistry,ELISA and liver enzyme analysis were performed to assess IRI following LT.Western blotting and quantitative reverse transcription-polymerase chain reaction were conducted to investigate the pertinent molecular changes.Results:Our findings revealed a significant increase in the expression of HSP110 at both the mRNA and protein levels in the rat liver following LT(P<0.05).However,when rats were injected with siRNAHSP110,IRI subsequent to LT was notably reduced(P<0.05).Additionally,the levels of liver enzymes and inflammatory chemokines in rat serum were significantly reduced(P<0.05).Silencing HSP110 with siRNA resulted in a marked decrease in M1-type polarization of Kupffer cells in the liver and downregulated the NF-κB pathway in the liver(P<0.05).Conclusions:HSP110 in the liver promotes IRI after LT in rats by activating the NF-κB pathway and inducing M1-type polarization of Kupffer cells.Targeting HSP110 to prevent IRI after LT may represent a promising new approach for the treatment of LT-associated IRI.

关键词： Ischemia-reperfusion injury Liver transplantation Inflammation HSP110 Heat shock proteins NF-κB

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Potential therapeutic role of spermine via Rac1 in osteoporosis:Insights from zebrafish and mice

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Zoological Research 2024年第2期45卷 367-380页

作者： rui-Xue Jiang Nan hu Yu-Wei Deng Long-Wei hu Hao Gu Nan Luo Jin Wen Xin-Quan Jiang Department of Prosthodontics Shanghai Ninth People’s HospitalShanghai Jiao Tong University School of MedicineShanghai 200011China College of Stomatology Shanghai Jiao Tong UniversityNational Center for StomatologyNational Clinical Research Center for Oral DiseasesShanghai Key Laboratory of StomatologyShanghai Research Institute of StomatologyShanghai Engineering Research Center of Advanced Dental Technology and MaterialsShanghai 200125China Department of Endodontics Shanghai Ninth People’s HospitalShanghai Jiao Tong University School of MedicineShanghai Jiao Tong UniversityShanghai 200011China Department of Oral and Maxillofacial-Head and Neck Oncology Shanghai Ninth People’s HospitalSchool of MedicineShanghai Jiao Tong UniversityShanghai 200011China Department of Preventive Dentistry Shanghai Ninth People’s HospitalShanghai Jiao Tong University School of MedicineShanghai Jiao Tong UniversityShanghai 200011China

Osteoporosis(OP)is a prevalent metabolic bone disease.While drug therapy is essential to prevent bone loss in osteoporotic patients,current treatments are limited by side effects and high costs,necessitating the development of more effective and safer targeted therapies.Utilizing a zebrafish(Danio rerio)larval model of osteoporosis,we explored the influence of the metabolite spermine on bone homeostasis.Results showed that spermine exhibited dual activity in osteoporotic zebrafish larvae by increasing bone formation and decreasing bone resorption.Spermine not only demonstrated excellent biosafety but also mitigated prednisolone-induced embryonic neurotoxicity and cardiotoxicity.Notably,spermine showcased protective attributes in the nervous systems of both zebrafish embryos and larvae.At the molecular level,Rac1 was identified as playing a pivotal role in mediating the antiosteoporotic effects of spermine,with P53 potentially acting downstream of Rac1.These findings were confirmed using mouse(Mus musculus)models,in which spermine not only ameliorated osteoporosis but also promoted bone formation and mineralization under healthy conditions,suggesting strong potential as a bonestrengthening agent.This study underscores the beneficial role of spermine in osteoporotic bone homeostasis and skeletal system development,highlighting pivotal molecular mediators.Given their efficacy and safety,human endogenous metabolites like spermine are promising candidates for new anti-osteoporotic drug development and daily bone-fortifying agents.

关键词： Osteoporosis Spermine Rac1 Zebrafish Mice

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