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Building Semantic Communication System via Molecules:An End-to-End Training Approach

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China Communications 2024年第7期21卷 113-124页

作者： Cheng Yukun Chen Wei Ai Bo School of Electronic and Information Engineering Beijing Jiaotong UniversityBeijing 100091China Frontiers Science center for Smart High-speed Railway System Beijing Jiaotong UniversityBeijing 100091China Key Laboratory of Railway Industry of Broadband Mobile Information Communications Beijing Jiaotong UniversityBeijing 100091China Beijing Engineering research center of High-speed Railway Broadband Mobile Communications Beijing Jiaotong UniversityBeijing 100091China School of Information Engineering Zhengzhou UniversityZhengzhou 450001China

The concept of semantic communication provides a novel approach for applications in scenarios with limited communication *** this paper,we propose an end-to-end(E2E)semantic molecular communication system,aiming to enhance the efficiency of molecular communication systems by reducing the transmitted ***,following the joint source channel coding paradigm,the network is designed to encode the task-relevant information into the concentration of the information molecules,which is robust to the degradation of the molecular communication ***,we propose a channel network to enable the E2E learning over the non-differentiable molecular *** results demonstrate the superior performance of the semantic molecular communication system over the conventional methods in classification tasks.

关键词： deep learning end-to-end learning molecular communication semantic communication

The lactylation index predicts the immune microenvironment and prognosis of pan-cancer patients

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BIOCELL 2024年第8期48卷 1223-1239页

作者： XUEJIA ZHAI JIE LIU JINWEI XIAO TAO ZHANG JUN WANG JIANJUN LI SHICANG YU Department of Oncology Southwest HospitalThird Military Medical University(Army Medical University)Chongqing400038China Department of Stem Cell and Regenerative Medicine Institute of Pathology and Southwest Cancer CenterSouthwest HospitalThird Military Medical University(Army Medical University)Chongqing400038China Key Laboratory of Cancer Immunopathology Ministry of EducationChongqing400038China International Joint research center for Precision Biotherapy Ministry of Science and TechnologyChongqing400038China Jin-feng Laboratory Chongqing401329China

Background:Protein lactylation is a new way for the“metabolic waste”lactic acid to perform novel ***,our understanding of the contribution of protein lactylation to both tumor progression and therapeutic interventions remains *** construction of a scoring system for lactylation to predict the prognosis of pancancer patients and to evaluate the tumor immune microenvironment(TIME)would improve our understanding of the clinical significance of ***:Consensus clustering analysis of lactylation-related genes was used to cluster 177 pancreatic adenocarcinoma(PAAD)***,a scoring system was developed using the least absolute shrinkage and selection operator(LASSO)*** validation and external validation were both conducted to assess and confirm the predictive accuracy of the scoring ***,leucine rich repeat containing 1(LRRC1),a newly discovered lactylation-related gene,was analyzed in PAAD in ***:Utilizing the profiles of 332 lactylation-related genes,a total of 177 patients with PAAD were segregated into two distinct ***^(high) patients had a poorer prognosis than LacCluster^(low) *** the differential analysis between the LacCluster^(high) and LacCluster^(low) groups,we identified additional genes associated with *** genes were then integrated to construct the LacCluster-enhanced system,which enabled more accurate prognosis prediction for patients with ***,a lactylation index containing three genes(LacI-3)was constructed using LASSO *** was done to enhance the usability of the LacCluster-enhanced system in the *** to those in the LacI-3^(high) subgroup,patients in the LacI-3^(low) subgroup exhibited increased expression of immune checkpoint-related genes,more immune cell infiltration,lower tumor mutation burdens,and better prognoses,indicating a“hot tumor”***,knocking down the expression of LRRC1,

关键词： Pancreatic adenocarcinoma Pan-cancer Lactylation Prognosis Tumor immune microenvironment LRRC1

Production and characterization of monoclonal antibodies against grass carp CD4-1 and CD4-2

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Aquaculture and Fisheries 2024年第2期9卷 154-163页

作者： Bangjie Wang Yuting Qin Zhaosheng Sun Xiaozhen Zhu Zhao Jia Kangyong Chen Danjie Liu Junya Wang Jun Zou Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources Ministry of EducationShanghai Ocean UniversityShanghai201306China International research center for Marine Biosciences at Shanghai Ocean University Ministry of Science and TechnologyShanghai201306China National Demonstration center for Experimental Fisheries Science Education Shanghai Ocean UniversityShanghai201306China Laboratory for Marine Biology and Biotechnology Qingdao National Laboratory for Marine Science and TechnologyQingdao266071China

CD4 T helper cells are an important group of cells in the immune system of vertebrates and express CD4 receptor on the cell *** mammals,the CD4 receptor is encoded by a single copy gene,whilst in fish,two copies of cd4 genes,namely cd4-1 and cd4-2,are *** this study,the ectodomains of grass carp(Ctenopharyngodon idella,Ci)CD4-1 and CD4-2 were expressed in the *** cells and used to generate monoclonal antibodies in *** blotting,confocal microscopy and flow cytometry were performed to characterize the monoclonal *** has been shown that the CiCD4-1 and CiCD4-2 monoclonal antibodies had good specificity to react with the recombinant ectodomains of CiCD4-1 and CiCD4-2 expressed in the CHO-S cells and the native CD4 molecules of grass *** CiCD4-1 monoclonal antibody did not recognize CiCD4-2 and verse *** addition,the CD4-1 and CD4-2 monoclonal antibodies specifically recognized the CD4-1 and CD4-2 receptors expressed in the HEK293 cells and native molecules of fish ***,the percentages of lymphocytes in immune tissues of healthy fish were analyzed by flow *** was found that 17.6%of lymphocytes were CD4-1^(+)cells and 22.5%were CD4-2^(+)in the head *** the spleen,13.1%of lymphocytes were CD4-1^(+)and 18.6%were CD4-2^(+)while 7.3%of blood lymphocytes were CD4-1^(+)cells and 8.8%were CD4-2^(+)*** availability of the CD4-1 and CD4-2 monoclonal antibodies provides antibody-based tools for further elucidation of the functions of CD4 T cells in grass carp.

关键词： Grass carp CD4 Monoclonal antibodies Flow cytometry Confocal microscopy

Feasibility study of the photonuclear reaction cross section of medical radioisotopes using a laser Compton scattering gamma source

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Nuclear Science and Techniques 2024年第9期35卷 168-177页

作者： Yu-Ning Gu Wei-Juan Zhao Xi-Guang Cao Yu-Xuan Yang Ting-Kai Ma Zheng-Li Liao Fei-Long Xu Yu-Gang Ma School of Physics and Microeletronics Zhengzhou UniversityZhengzhou 450001China Shanghai Advanced research Institute Chinese Academy of SciencesShanghai 201210China Shanghai Institute of Applied Physics Chinese Academy of SciencesShanghai 201800China University of Chinese Academy of Sciences Beijing 100049China School of Nuclear Science and Technology University of South ChinaHengyang 421001China Key Laboratory of Nuclear Physics and Ion-beam Application(MOE) Institute of Modern PhysicsFudan UniversityShanghai 200433China Shanghai research center for Theoretical Nuclear Physics NSFC and Fudan UniversityShanghai 200438China

In recent years,the gap between the supply and demand of medical radioisotopes has increased,necessitating new methods for producing medical *** reactions based on gamma sources have unique advantages in terms of producing high specific activity and innovative medical ***,the lack of experimental data on reaction cross sections for photonuclear reactions of medical radioisotopes of interest has severely limited the development and production of photonuclear transmutation medical *** this study,the entire process of the generation,decay,and measurement of medical radioisotopes was simulated using online gamma activation and offline gamma measurements combined with a shielding gamma-ray *** on a quasi-monochromatic gamma beam from the Shanghai Laser Electron Gamma Source(SLEGS),the feasibility of this measurement of production cross section for surveyed medi-cal radioisotopes was simulated,and specific solutions for measuring medical radioisotopes with ultra-low production cross sections were *** feasibility of this method for high-precision measurements of the reaction cross section of medical radioisotopes was demonstrated.

关键词： Medical radioisotope Photonuclear reaction GEANT4 Shanghai Laser Electron Gamma Source(SLEGS) Low-background gamma-ray spectrometer

Targeting miRNA by CRISPR/Cas in cancer:advantages and challenges

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Military Medical research 2024年第3期11卷 345-373页

作者： Bashdar Mahmud Hussen Mohammed Fatih Rasul Snur Rasool Abdullah Hazha Jamal Hidayat Goran Sedeeq Hama Faraj Fattma Abodi Ali Abbas Salihi Aria Baniahmad Soudeh Ghafouri-Fard Milladur Rahman Mark C.Glassy Wojciech Branicki Mohammad Taheri Department of Biomedical Sciences Cihan University-ErbilErbilKurdistan Region 44001Iraq Department of Clinical Analysis College of PharmacyHawler Medical UniversityErbilKurdistan Region 44001Iraq Department of Pharmaceutical Basic Science Faculty of PharmacyTishk International UniversityErbilKurdistan Region 44001Iraq Medical Laboratory Science Lebanese French UniversityErbilKurdistan Region 44001Iraq Department of Biology College of EducationSalahaddin University-ErbilErbilKurdistan Region 44001Iraq Department of Medical Laboratory Science Komar University of Science and TechnologySulaymaniyah 46001Iraq Department of Medical Microbiology College of Health SciencesHawler Medical UniversityErbilKurdistan Region 44001Iraq Department of Biology College of ScienceSalahaddin University-ErbilErbilKurdistan Region 44001Iraq center of research and Strategic Studies Lebanese French UniversityErbil 44001Iraq Institute of Human Genetics Jena University Hospital07747 JenaGermany Department of Medical Genetics School of MedicineShahid Beheshti University of Medical SciencesTehran 374-37515Iran Department of Clinical Sciences MalmöSection for SurgeryLund University22100 MalmöSweden Translational Neuro-Oncology Laboratory San Diego(UCSD)Moores Cancer CenterUniversity of CaliforniaSan DiegoCA 94720USA Faculty of Biology Institute of Zoology and Biomedical ResearchJagiellonian University31-007 KrakówPoland Urology and Nephrology research center Shahid Beheshti University of Medical SciencesTehran 374-37515Iran

Clustered regulatory interspaced short palindromic repeats(CRISPR)has changed biomedical research and provided entirely new models to analyze every aspect of biomedical sciences during the last *** the study of cancer,the CRISPR/CRISPR-associated protein(Cas)system opens new avenues into issues that were once unknown in our knowledge of the non-coding genome,tumor heterogeneity,and precision ***/Cas-based geneediting technology now allows for the precise and permanent targeting of mutations and provides an opportunity to target small non-coding RNAs such as microRNAs(miRNAs).However,the development of effective and safe cancer gene editing therapy is highly dependent on proper design to be innocuous to normal cells and prevent introducing other *** study aims to highlight the cutting-edge approaches in cancer-gene editing therapy based on the CRISPR/Cas technology to target miRNAs in cancer ***,we highlight the potential challenges in CRISPR/Cas-mediated miRNA gene editing and offer advanced strategies to overcome them.

关键词： CRISPR CRISPR/Cas9 CRISPR/Cas12 Gene editing miRNAs Cancer therapy

Efficient and accurate simulation of vitrification in multicomponent metallic liquids with neural network potentials

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Science China Materials 2024年第10期67卷 3298-3308页

作者： Rui Su Jieyi Yu Pengfei Guan Weihua Wang College of Materials&Environmental Engineering Hangzhou Dianzi UniversityHangzhou 310018China Beijing Computational Science research center Beijing 100193China Songshan Lake Materials Laboratory Dongguan 523808China

Constructing an accurate interatomic potential and overcoming the exponential growth of structural equilibration time are challenges for atomistic investigations of the composition-dependent structure and dynamics during the vitrification process of deeply supercooled multicomponent metallic *** this work,we describe a state-of-the-art strategy to address these challenges *** the case of the representative Zr–Cu–Al system,in combination with a general algorithm for effectively and accurately generating the neural network potentials(NNPs)of multicomponent metallic glasses,we propose a highly efficient atom-swapping hybrid Monte Carlo(SHMC)algorithm for accelerating the thermodynamic equilibration of deeply supercooled *** calculations demonstrate that the newly developed NNP faithfully reproduces the phase stabilities and structural characteristics obtained from ab initio calculations and *** the combined NNP-SHMC algorithm,the structure equilibration time at deeply supercooled temperatures is accelerated by at least five orders of magnitude,and the quenched glassy samples exhibit comparable stability to those prepared in the *** results pave the way for next-generation studies of the vitrification process and,thereby,the composition-dependent glass-forming ability and physical properties of multicomponent metallic glasses.

关键词： metallic glass computational methods glass transition

TMB相关免疫浸润调控评分(MOTIF)预测免疫治疗响应并指导联合增效

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Science Bulletin 2024年第6期69卷 803-822页

作者：钱政宇潘艺芊李薛鑫陈衍行吴灏祥刘泽先 Martin Kosar Jiri Bartek 王梓贤徐瑞华 Department of Medical Oncology Sun Yat-sen University Cancer CenterState Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer MedicineGuangdong Provincial Clinical Research Center for CancerResearch Unit of Precision Diagnosis and Treatment for Gastrointestinal CancerChinese Academy of Medical SciencesGuangzhou 510060China Science for Life Laboratory Division of Genome BiologyDepartment of Medical Biochemistry and BiophysicsKarolinska InstituteStockholm S-17121Sweden Department of General Surgery The Fourth Affiliated HospitalChina Medical UniversityShenyang 110032China Bioinformatics Platform Sun Yat-sen University Cancer CenterGuangzhou 510060China Zhejiang University-University of Edinburgh Institute Zhejiang University School of MedicineHaining 314400China Edinburgh Medical School Biomedical SciencesCollege of Medicine and Veterinary MedicineThe University of EdinburghEdinburgh EH11LTUK Danish Cancer Society research center Copenhagen DK-2100Denmark Laboratory of Artificial Intelligence and Data Science Sun Yat-sen University Cancer CenterGuangzhou 510060China

Patients with high tumor mutational burden(TMB)levels do not consistently respond to immune checkpoint inhibitors(ICIs),possibly because a high TMB level does not necessarily result in adequate infiltration of CD8^(+)T *** bulk ribonucleic acid sequencing(RNA-seq)data from 9311 tumor samples across 30 cancer types,we developed a novel tool called the modulator of TMB-associated immune infiltration(MOTIF),which comprises genes that can determine the extent of CD8^(+)T cell infiltration prompted by a certain TMB *** confirmed that MOTIF can accurately reflect the integrity and defects of the cancer-immunity *** analyzing 84 human single-cell RNA-seq datasets from 32 types of solid tumors,we revealed that MOTIF can provide insights into the diverse roles of various cell types in the modulation of CD8^(+)T cell *** pretreatment RNA-seq data from 13 ICI-treated cohorts,we validated the use of MOTIF in predicting CD8^(+)T cell infiltration and ICI *** the components of MOTIF,we identified EMC3 as a negative regulator of CD8^(+)T cell infiltration,which was validated via in vivo ***,MOTIF provided guidance for the potential combinations of programmed death 1 blockade with certain immunostimulatory drugs to facilitate CD8^(+)T cell infiltration and improve ICI efficacy.

关键词： Tumor mutational burden Immunotherapy Cancer-immunity cycle Treatment efficacy prediction CD8^(+)T cell infiltration Combination therapy

Accclerating thc Devclopmcnt of New Quality Productive Forces with a Focus on High-Quality Development

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Qiu Shi 2024年第3期16卷 41-50页

作者： Zhang Laiming Development research center of the State Council

Gaining a sound understanding of new quality productive forces and accelerating their development holds important theoretical and practical significance for high-quality development.

关键词： Focus holds Quality

Visualization analysis of research hotspots and trends on gastrointestinal tumor organoids

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World Journal of Gastrointestinal Oncology 2024年第6期16卷 2826-2841页

作者： Gang Wang Tao Liu Wen-Ting He School of Basic Medical Sciences Lanzhou UniversityLanzhou 730000Gansu ProvinceChina Digestive System Tumor Prevention and Treatment and Translational Medicine Engineering Innovation center of Lanzhou University Lanzhou UniversityLanzhou 730000Gansu ProvinceChina Digestive System Tumor Translational Medicine Engineering research center of Gansu Province Lanzhou UniversityLanzhou 730000Gansu ProvinceChina The Second Hospital&Clinical Medical School Lanzhou UniversityLanzhou 730030Gansu ProvinceChina

BACKGROUND Gastrointestinal tumor organoids serve as an effective model for simulating cancer in vitro and have been applied in basic biology and preclinical *** over a decade of development and increasing research achievements in this field,a systematic and comprehensive analysis of the research hotspots and future trends is *** To address this problem by employing bibliometric tools to explore the publication years,countries/regions,institutions,journals,authors,keywords,and references in this *** The literature was collected from Web of Science ***-6.2R4,a widely used bibliometric analysis software package,was used for institutional analysis and reference burst *** 1.6.19 was used for journal cocitation analysis,author co-authorship and co-citation ***‘online platform for bibliometric analysis(https://***/app)’was used to assess the total number of publications and the cooperation relationships between ***,we employed the bibliometric R software package(version R.4.3.1)in R-studio,for a comprehensive scientific analysis of the *** Our analysis included a total of 1466 publications,revealing a significant yearly increase in articles on the study of gastrointestinal tumor *** United States(n=393)and Helmholtz Association(n=93)have emerged as the leading countries and institutions,respectively,in this field,with Hans Clevers and Toshiro Sato being the most contributing *** most influential journal in this field is *** most impactful reference is"Long term expansion of epithelial organs from human colon,adenoma,adenocarcinoma,and Barrett's epithelium".Keywords analysis and citation burst analysis indicate that precision medicine,disease modeling,drug development and screening,and regenerative medicine are the most cutting-edge *** focal points were further detailed based on the *** This bibl

关键词： Gastrointestinal tumor organoids Bibliometric analysis Drug development and screening Model CiteSpace