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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

Customization of FeNi alloy nanosheet arrays inserted with biomass-derived carbon templates for boosted electromagnetic wave absorption

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International Journal of Minerals,Metallurgy and Materials 2024年第4期31卷 812-824页

作者： Xuanqi Yang Honghan Wang jing Chen Qingda An Zuoyi Xiao jingai Hao Shangru zhai Junye Sheng Liaoning Key Lab of Lignocellulose Chemistry and BioMaterials Liaoning Collaborative Innovation Center for Lignocellulosic BiorefineryCollege of Light Industry and Chemical EngineeringDalian Polytechnic UniversityDalian 116034China Qingdao Medical College Qingdao UniversityQingdao 266071China

Electromagnetic wave(EMW)-absorbing materials have considerable capacity in the military field and the prevention of EMW radiation from harming human health.However,obtaining lightweight,high-performance,and broadband EMW-absorbing material remains an overwhelming challenge.Creating dielectric/magnetic composites with customized structures is a strategy with great promise for the development of high-performance EMW-absorbing materials.Using layered double hydroxides as the precursors of bimetallic alloys and combining them with porous biomass-derived carbon materials is a potential way for constructing multi-interface heterostructures as efficient EMW-absorbing materials because they have synergistic losses,low costs,abundant resources,and light weights.Here,FeNi alloy nanosheet array/Lycopodium spore-derived carbon(FeNi/LSC)was prepared through a simple hydrothermal and carbonization method.FeNi/LSC presents ideal EMW-absorbing performance by benefiting from the FeNi alloy nanosheet array,sponge-like structure,capability for impedance matching,and improved dielectric/magnetic losses.As expected,FeNi/LSC exhibited the minimum reflection loss of-58.3 dB at 1.5 mm with 20wt%filler content and a widely effective absorption bandwidth of 4.92 GHz.FeNi/LSC composites with effective EMW-absorbing performance provide new insights into the customization of biomass-derived composites as high-performance and lightweight broadband EMW-absorbing materials.

关键词： spore-derived carbon FeNi alloy nanosheet array multi-interface heterostructures synergistic effect efficient electromagnet-ic wave absorption

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 trigger system on experimental dispersion characteristics of active surface wave testing

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Earthquake Engineering and Engineering Vibration 2024年第2期23卷 311-318页

作者： Lin Shibin Jeramy C.Ashlock Zhu Liming Qin Zexiang Li bo Zhu Xingji zhai Changhai State Key Laboratory of Precision Blasting Jianghan UniversityWuhan 430056China Hubei Key Laboratory of Blasting Engineering Jianghan UniversityWuhan 430056China Department of Civil Construction&Environmental EngineeringIowa State UniversityAmesIA 50010USA Wuhan Airport Road Development Co. Ltd.Wuhan 430065China School of Civil and Environmental Engineering Harbin Institute of TechnologyShenzhen 518055China Key Lab of Structures Dynamic Behavior and Control of the Ministry of Education Harbin Institute of TechnologyHarbin 150090China Key Lab of Smart Prevention and Mitigation of Civil Engineering Disaster of the Ministry of Industry and Information Technology Harbin Institute of TechnologyHarbin 150090China

A trigger system is typically employed in active seismic testing to trigger and synchronize multichannel surface wave data acquisition.The effect of the trigger system on the dispersion image of surface waves is empirically known to be negligible,however,theoretical explanation regarding the effect of the trigger system is insufficient.This study systematically examines the theory for surface wave dispersion analysis and proves that the effect of the trigger system on a dispersion image is negligible via a solid theoretical explanation.Subsequently,based on the new theoretical explanation,an alternative method that uses only the relative phase difference between sensors to extract dispersion characteristics with better conceptual clarity is proposed.Two active surface wave testing cases are considered to validate the theory and method.The results indicate that(1)an accurate trigger system is not necessary for surface wave data acquisition,and(2)it is unnecessary to assume that the impact point is the generation point of the surface waves for the experimental dispersion analysis.

关键词： site investigation surface waves data acquisition dispersion

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