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Single-cell RNA sequencing to understand host-virus interactions

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Virologica Sinica 2024年第1期39卷 1-8页

作者： Jia-Tong Chang Li-bo Liu Pei-Gang Wang jing An Department of Microbiology School of Basic Medical SciencesCapital Medical UniversityBeijing 100069China

Single-cell RNA sequencing(scRNA-seq)has allowed for the profiling of host and virus transcripts and host-virus interactions at single-cell resolution.This review summarizes the existing scRNA-seq technologies together with their strengths and weaknesses.The applications of scRNA-seq in various virological studies are discussed in depth,which broaden the understanding of the immune atlas,host-virus interactions,and immune repertoire.scRNA-seq can be widely used for virology in the near future to better understand the pathogenic mechanisms and discover more effective therapeutic strategies.

关键词： Single-cell RNA sequencing(scRNA-seq) Host-virus interaction COVID-19 Flavivirus

A Knowledge-enhanced Two-stage Generative Framework for Medical Dialogue Information Extraction

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Machine Intelligence Research 2024年第1期21卷 153-168页

作者： Zefa Hu Ziyi Ni jing Shi Shuang Xu bo Xu School of Artificial Intelligence University of Chinese Academy of SciencesBeijing 100049China Institute of Automation Chinese Academy of SciencesBeijing 100190China

This paper focuses on term-status pair extraction from medical dialogues(MD-TSPE),which is essential in diagnosis dia-logue systems and the automatic scribe of electronic medical records(EMRs).In the past few years,works on MD-TSPE have attracted increasing research attention,especially after the remarkable progress made by generative methods.However,these generative methods output a whole sequence consisting of term-status pairs in one stage and ignore integrating prior knowledge,which demands a deeper un-derstanding to model the relationship between terms and infer the status of each term.This paper presents a knowledge-enhanced two-stage generative framework(KTGF)to address the above challenges.Using task-specific prompts,we employ a single model to com-plete the MD-TSPE through two phases in a unified generative form:We generate all terms the first and then generate the status of each generated term.In this way,the relationship between terms can be learned more effectively from the sequence containing only terms in the first phase,and our designed knowledge-enhanced prompt in the second phase can leverage the category and status candidates of the generated term for status generation.Furthermore,our proposed special status"not mentioned"makes more terms available and en-riches the training data in the second phase,which is critical in the low-resource setting.The experiments on the Chunyu and CMDD datasets show that the proposed method achieves superior results compared to the state-of-the-art models in the full training and low-re-sourcesettings.

关键词： Medical dialogue understanding information extraction text generation knowledge-enhanced prompt low-resource setting dataaugmentation

Flexible tuning of multifocal holographic imaging based on electronically controlled metasurfaces

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Photonics Research 2024年第1期12卷 61-69页

作者： OWEN ZENG CHENXIA LI bo FANG ZHI HONG XUFENG jing Institute of Optoelectronic Technology China Jiliang UniversityHangzhou 310018China Centre for THz Research China Jiliang UniversityHangzhou 310018China College of Metrology&Measurement Engineering China Jiliang UniversityHangzhou 310018China

Programmable hyper-coded holography has the advantage of being programmable as well as being flexibly modifiable.Digitally coded metamaterials with excellent electromagnetic modulation capability and the ability to control the phase to modulate the spatial radiation field through external excitation in the form of switching can be used to realize low-cost digital arrays.We design a 1-bit encoded programmable metasurface,which is electrically connected to control the PIN diode in the switching state and to switch the condition of each metasurface cell between“0”and“1.”Using the designed programmable metasurface,we can randomly encode the cell structure to realize single-focus focusing,multi-focusing,and simple holographic letter imaging.Based on the nonlinear holographic model,we employ the Gerchberg-Saxton improvement algorithm to modulate the energy distribution at the focus by adjusting the phase distribution.Importantly,we introduce the Fourier convolution principle to regulate the holographic imaging focus flexibly.

关键词： holographic letter excitation

Macrocyclic peptides:up-and-coming weapons to combat antimicrobial resistance

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Signal Transduction and Targeted Therapy 2024年第5期9卷 1786-1787页

作者： Wen-jing Wang Xiang-Min Dong Guo-bo L Department of Biotherapy Cancer Center and State Key Laboratory of BiotherapyWest China HospitalSichuan UniversityChengduSichuanChina Key Laboratory of Drug Targeting and Drug Delivery System of Ministry of Education Department of Medicinal ChemistryWest China School of PharmacySichuan UniversityChengduSichuanChina

Recently,two companion papers published in Nature reported a first-in-class tethered macrocyclic peptide antibiotic targeting carbapenem-resistant A.baumannii(CRAB)and unveiled their unique antibacterial mechanism,whi... 详细信息

关键词： outer macrocyclic Macrocyclic

Corporate Credit Ratings Based on Hierarchical Heterogeneous Graph Neural Networks

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Machine Intelligence Research 2024年第2期21卷 257-271页

作者： bo-jing Feng Xi Cheng Hao-Nan Xu Wen-Fang Xue Center for Research on Intelligent Perception and Computing National Laboratory of Pattern RecognitionInstitute of AutomationChinese Academy of SciencesBeijing 100190China

order to help investors understand the credit status of target corporations and reduce investment risks,the corporate credit rating model has become an important evaluation tool in the financial market.These models are based on statistical learning,machine learning and deep learning especially graph neural networks(GNNs).However,we found that only few models take the hierarchy,heterogeneity or unlabeled data into account in the actual corporate credit rating process.Therefore,we propose a novel framework named hierarchical heterogeneous graph neural networks(HHGNN),which can fully model the hierarchy of corporate features and the heterogeneity of relationships between corporations.In addition,we design an adversarial learning block to make full use of the rich unlabeled samples in the financial data.Extensive experiments conducted on the public-listed corporate rating dataset prove that HHGNN achieves SOTA compared to the baseline methods.

关键词： Corporate credit rating hierarchical relation heterogeneous graph neural networks adversarial learning

Effect of aflibercept combined with triamcinolone acetonide on aqueous humor growth factor and inflammatory mediators in diabetic macular edema

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International Journal of Ophthalmology(English edition) 2024年第2期17卷 297-303页

作者： De-Shuang Li Hong-Xia Liao jing-Lin Zhang bo Qin Shenzhen Aier Eye Hospital Aier Eye HospitalJinan UniversityShenzhen 518031Guangdong ProvinceChina Guangzhou Aier Eye Hospital Jinan UniversityGuangzhou 510040Guangdong ProvinceChina

AIM:To investigate the efficacy of aflibercept combined with sub-tenon injection of triamcinolone acetonide(TA)in treating diabetic macular edema(DME)and to examine changes in growth factors and inflammatory mediator levels in aqueous humor after injection.METHODS:Totally 67 DME patients(67 eyes)and 30 cataract patients(32 eyes)were enrolled as the DME group and the control group,respectively.The DME group was divided into the aflibercept group(34 cases)and the aflibercept combined with TA group(combined group,33 cases).The aqueous humor of both groups was collected during the study period.The aqueous levels of vascular endothelial growth factor(VEGF),monocyte chemoattractant protein-1(MCP-1),interleukin-6(IL-6),interleukin-8(IL-8),and interleukin-1β(IL-1β)were detected using a microsphere suspension array technology(Luminex 200TM).Aqueous cytokines,best-corrected visual acuity(BCVA),central macular thickness(CMT),and complications before and after treatment were compared between the aflibercept group and combined group.RESULTS:The concentrations of VEGF,MCP-1,IL-6,and IL-8 in the aqueous humor were significantly higher in the DME group than those of the control group(all P0.05).CONCLUSION:The cytokines VEGF,MCP-1,IL-6,and IL-8 in the aqueous humor of DME patients are significantly increased.Aflibercept and aflibercept combined with TA have good efficacy in DME patients,can effectively reduce CMT,improve the patient’s vision,and have high safety.Aflibercept combined with TA can quickly downregulate the aqueous humor cytokines and help to relieve macular edema rapidly.However,the long-term efficacy is comparable to that of aflibercept alone

关键词： diabetic macular edema aqueous humor cytokines aflibercept triamcinolone acetonide

A novel structural variant of RET causes familial Hirschsprung's disease via nonsense-mediated mRNA decay

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Genes & Diseases 2024年第1期11卷 7-10页

作者： Qi Wang Siyu Pu bo Xiang jing Chen Department of Pediatric Surgery and Laboratory of Pediatric Surgery Rare Diseases CenterInstitute of Immunology and InflammationFrontiers Science Center for Disease-Related Molecular NetworkWest China HospitalSichuan UniversityChengduSichuan 610041China

Hirschsprung's disease(HsCR)is the most common type of developmental gastrointestinal malformation causing intestinal obstruction in children,with an incidence of 1/5000 in live births.1 it is characterized by the absence of intrinsic ganglion cells in the myenteric and submucosal plexuses of the distal gastrointestinal tract,leading to the dysregulation of smooth muscle contraction/relaxation and resulting in intestinal obstruction.Depending on the length of the aganglionic intestine,HSCR can be categorized into short-segmental HSCR(S-HSCR),which affects up to the sigmoid colon from the anus,and long-segmental HSCR(LHSCR),which affects beyond the sigmoid colon.1 In some rare conditions,aganglionic lesions can affect the full length of the colon or even the whole intestine.

关键词： intestine colon relaxation

Communication efficiency optimization of federated learning for computing and network convergence of 6G networks

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Frontiers of Information Technology & Electronic Engineering 2024年第5期25卷 713-727页

作者： Yizhuo CAI bo LEI Qianying ZHAO jing PENG Min WEI Yushun ZHANG Xing ZHANG Wireless Signal Processing and Network Laboratory Beijing University of Posts and TelecommunicationsBeijing 100876China Research Institute of China Telecom Co. Ltd.Beijing 102209China Beijing Telecom Beijing 100011China

Federated learning effectively addresses issues such as data privacy by collaborating across participating devices to train global models.However,factors such as network topology and computing power of devices can affect its training or communication process in complex network environments.Computing and network convergence(CNC)of sixth-generation(6G)networks,a new network architecture and paradigm with computing-measurable,perceptible,distributable,dispatchable,and manageable capabilities,can effectively support federated learning training and improve its communication efficiency.By guiding the participating devices'training in federated learning based on business requirements,resource load,network conditions,and computing power of devices,CNC can reach this goal.In this paper,to improve the communication eficiency of federated learning in complex networks,we study the communication eficiency optimization methods of federated learning for CNC of 6G networks that give decisions on the training process for different network conditions and computing power of participating devices.The simulations address two architectures that exist for devices in federated learning and arrange devices to participate in training based on arithmetic power while achieving optimization of communication efficiency in the process of transferring model parameters.The results show that the methods we proposed can cope well with complex network situations,effectively balance the delay distribution of participating devices for local training,improve the communication eficiency during the transfer of model parameters,and improve the resource utilization in the network.

关键词： Computing and network convergence Communication efficiency Federated learning Two architectures

Size-dependent thermomechanical vibration characteristics of rotating pre-twisted functionally graded shear deformable microbeams

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Applied Mathematics and Mechanics(English Edition) 2024年第6期45卷 1015-1032页

作者： Songye JIN bo ZHANG Wuyuan ZHANG Yuxing WANG Huoming SHEN jing WANG Juan LIU School of Mechanics and Aerospace Engineering Southwest Jiaotong UniversityChengdu 610031China School of Mechanical Engineering Southwest Jiaotong UniversityChengdu 610031China School of Mechanical and Electrical Engineering Southwest Petroleum UniversityChengdu 610500China

A three-dimensional(3D)thermomechanical vibration model is developed for rotating pre-twisted functionally graded(FG)microbeams according to the refined shear deformation theory(RSDT)and the modified couple stress theory(MCST).The material properties are assumed to follow a power-law distribution along the chordwise direction.The model introduces one axial stretching variable and four transverse deflection variables including two pure bending components and two pure shear ones.The complex modal analysis and assumed mode methods are used to solve the governing equations of motion under different boundary conditions(BCs).Several examples are presented to verify the effectiveness of the developed model.By coupling the slenderness ratio,gradient index,rotation speed,and size effect with the pre-twisted angle,the effects of these factors on the thermomechanical vibration of the microbeam with different BCs are investigated.It is found that with the increase in the pre-twisted angle,the critical slenderness ratio and gradient index corresponding to the thermal instability of the microbeam increase,while the critical material length scale parameter(MLSP)and rotation speed decrease.The sensitivity of the fundamental frequency to temperature increases with the increasing slenderness ratio and gradient index,and decreases with the other increasing parameters.Moreover,the size effect can suppress the dynamic stiffening effect and enhance the Coriolis effect.Finally,the mode transition is quantitatively demonstrated by a modal assurance criterion(MAC).

关键词： thermomechanical vibration rotating pre-twisted functionally graded(FG)microbeam refined shear deformation theory(RSDT) modified couple stress theory(MCST) modal assurance criterion(MAC)