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Construction of an immune-related gene signature for overall survival prediction and immune infiltration in gastric cancer

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World Journal of Gastrointestinal Oncology 2024年第3期16卷 919-932页

作者： xiao-Ting Ma Xiu Liu Kai Ou lin yang Department of Medical Oncology Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing 100021China

BACKGROUND Treatment options for patients with gastric cancer(GC)continue to improve,but the overall prognosis is poor.The use of PD-1 inhibitors has also brought benefits to patients with advanced GC and has gradually become the new standard treatment option at present,and there is an urgent need to identify valuable biomarkers to classify patients with different characteristics into subgroups.AIM To determined the effects of differentially expressed immune-related genes(DEIRGs)on the development,prognosis,tumor microenvironment(TME),and treatment response among GC patients with the expectation of providing new biomarkers for personalized treatment of GC populations.METHODS Gene expression data and clinical pathologic information were downloaded from The Cancer Genome Atlas(TCGA),and immune-related genes(IRGs)were searched from ImmPort.DEIRGs were extracted from the intersection of the differentially-expressed genes(DEGs)and IRGs lists.The enrichment pathways of key genes were obtained by analyzing the Kyoto Encyclopedia of Genes and Genomes(KEGGs)and Gene Ontology(GO)databases.To identify genes associated with prognosis,a tumor risk score model based on DEIRGs was constructed using Least Absolute Shrinkage and Selection Operator and multivariate Cox regression.The tumor risk score was divided into high-and lowrisk groups.The entire cohort was randomly divided into a 2:1 training cohort and a test cohort for internal validation to assess the feasibility of the risk model.The infiltration of immune cells was obtained using‘CIBERSORT,’and the infiltration of immune subgroups in high-and low-risk groups was analyzed.The GC immune score data were obtained and the difference in immune scores between the two groups was analyzed.RESULTS We collected 412 GC and 36 adjacent tissue samples,and identified 3627 DEGs and 1311 IRGs.A total of 482 DEIRGs were obtained.GO analysis showed that DEIRGs were mainly distributed in immunoglobulin complexes,receptor ligand activity,and signaling receptor activators.KEGG pathway analys

关键词： Differentially expressed immune-related gene Immunotherapy Gastric cancer Risk score

A CAD-BEM geometry transformation method for face-based primary geometric input based on closed contour recognition

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Building Simulation 2024年第2期17卷 335-354页

作者： Jun xiao Hao Zhou Shiji yang Deyin Zhang Borong lin Department of Building Science School of ArchitectureTsinghua UniversityBeijing100084China Key Laboratory of Eco Planning&Green Building Ministry of EducationTsinghua UniversityBeijing100084China Institute for Urban Governance and Sustainable Development Tsinghua UniversityBeijing100084China

Performance analysis during the early design stage can significantly reduce building energy consumption.However,it is difficult to transform computer-aided design(CAD)models into building energy models(BEM)to optimize building performance.The model structures for CAD and BEM are divergent.In this study,geometry transformation methods was implemented in BES tools for the early design stage,including auto space generation(ASG)method based on closed contour recognition(CCR)and space boundary topology calculation method.The program is developed based on modeling tools SketchUp to support the CAD format(like*.stl,*.dwg,*.ifc,etc.).It transforms face-based geometric information into a zone-based tree structure model that meets the geometric requirements of a single-zone BES combined with the other thermal parameter inputs of the elements.In addition,this study provided a space topology calculation method based on a single-zone BEM output.The program was developed based on the SketchUp modeling tool to support additional CAD formats(such as*.stl,*.dwg,*.ifc),which can then be imported and transformed into*.obj.Compared to current methods mostly focused on BIM-BEM transformation,this method can ensure more modeling flexibility.The method was integrated into a performance analysis tool termed MOOSAS and compared with the current version of the transformation program.They were tested on a dataset comprising 36 conceptual models without partitions and six real cases with detailed partitions.It ensures a transformation rate of two times in any bad model condition and costs only 1/5 of the time required to calculate each room compared to the previous version.

关键词： geometry transformation building energy model computer aid design closed contour recognition

Metabolomic Analysis in Saliva and Different Brain Regions of Older Mice with Postoperative Delirium Behaviors

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Biomedical and Environmental Sciences 2024年第2期37卷 133-145页

作者： LIU xiao CAO Ying lin xiao Wan GAO Dan yang MIAO Hui Hui LI Tian Zuo Department of Anesthesiology Beijing Shijitan HospitalCapital Medical UniversityBeijing 100038China

Objective Postoperative delirium(POD)has become a critical challenge with severe consequences and increased incidences as the global population ages.However,the underlying mechanism is yet unknown.Our study aimed to explore the changes in metabolites in three specific brain regions and saliva of older mice with postoperative delirium behavior and to identify potential non-invasive biomarkers.Methods Eighteen-month-old male C57/BL6 mice were randomly assigned to the anesthesia/surgery or control group.Behavioral tests were conducted 24 h before surgery and 6,9,and 24 h after surgery.Complement C3(C3)and S100 calcium-binding protein B protein(S100beta)levels were measured in the hippocampus,and a metabolomics analysis was performed on saliva,hippocampus,cortex,and amygdala samples.Results In total,43,33,38,and 14 differential metabolites were detected in the saliva,hippocampus,cortex,and amygdala,respectively.“Pyruvate”“alpha-linolenic acid”and“2-oleoyl-1-palmitoy-snglycero-3-phosphocholine”are enriched in one common pathway and may be potential non-invasive biomarkers for POD.Common changes were observed in the three brain regions,with the upregulation of 1-methylhistidine and downregulation of D-glutamine.Conclusion Dysfunctions in energy metabolism,oxidative stress,and neurotransmitter dysregulation are implicated in the development of POD.The identification of changes in the level of salivary metabolite biomarkers could aid in the development of noninvasive diagnostic methods for POD.

关键词： Metabolomic Postoperative delirium(POD) Mechanism Biological marker

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Single-cell profiling of the pig cecum at various developmental stages

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Zoological Research 2024年第1期45卷 55-68页

作者： Yan-Yuan xiao Qing Zhang Fei Huang lin Rao Tian-Xiong Yao Si-Yu yang Lei Xie xiao-xiao Zou Li-Ping Cai Jia-Wen yang Bin yang Lu-Sheng Huang National Key Laboratory for Swine Genetic Improvement and Germplasm Innovation Ministry of Science and Technology of ChinaJiangxi Agricultural UniversityNanchangJiangxi 330045China

The gastrointestinal tract is essential for food digestion,nutrient absorption,waste elimination,and microbial defense.Single-cell transcriptome profiling of the intestinal tract has greatly enriched our understanding of cellular diversity,functional heterogeneity,and their importance in intestinal tract development and disease.Although such profiling has been extensively conducted in humans and mice,the single-cell gene expression landscape of the pig cecum remains unexplored.Here,single-cell RNA sequencing was performed on 45572 cells obtained from seven cecal samples in pigs at four different developmental stages(days(D)30,42,150,and 730).Analysis revealed 12 major cell types and 38 subtypes,as well as their distinctive genes,transcription factors,and regulons,many of which were conserved in humans.An increase in the relative proportions of CD8^(+)T and Granzyme A(low expression)natural killer T cells(GZMA^(low)NKT)cells and a decrease in the relative proportions of epithelial stem cells,Tregs,RHEX^(+)T cells,and plasmacytoid dendritic cells(pDCs)were noted across the developmental stages.Moreover,the post-weaning period exhibited an up-regulation in mitochondrial genes,COX2 and ND2,as well as genes involved in immune activation in multiple cell types.Cell-cell crosstalk analysis indicated that IBP6^(+)fibroblasts were the main signal senders at D30,whereas IBP6^(−)fibroblasts assumed this role at the other stages.NKT cells established interactions with epithelial cells and IBP6^(+)fibroblasts in the D730 cecum through mediation of GZMA-F2RL1/F2RL2 pairs.This study provides valuable insights into cellular heterogeneity and function in the pig cecum at different development stages.

关键词： Single-cell RNA-seq Cecum Bama Xiang pigs Various developmental stages Cellular heterogeneity

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Diabetes and high-glucose could upregulate the expression of receptor for activated C kinase 1 in retina

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World Journal of Diabetes 2024年第3期15卷 519-529页

作者： Jian Tan Ang xiao lin yang Yu-lin Tao Yi Shao Qiong Zhou Department of Ophthalmology The First Affiliated HospitalJiangxi Medical CollegeNanchang UniversityNanchang 330006Jiangxi ProvinceChina

BACKGROUND Diabetic retinopathy(DR)is a major ocular complication of diabetes mellitus,leading to visual impairment.Retinal pigment epithelium(RPE)injury is a key component of the outer blood retinal barrier,and its damage is an important indicator of DR.Receptor for activated C kinase 1(RACK1)activates protein kinase C-ε(PKC-ε)to promote the generation of reactive oxygen species(ROS)in RPE cells,leading to apoptosis.Therefore,we hypothesize that the activation of RACK1 under hypoxic/high-glucose conditions may promote RPE cell apoptosis by modulating PKC-ε/ROS,thereby disrupting the barrier effect of the outer blood retinal barrier and contributing to the progression of DR.AIM To investigate the role and associated underlying mechanisms of RACK1 in the development of early DR.METHODS In this study,Sprague-Dawley rats and adult RPE cell line-19(ARPE-19)cells were used as in vivo and in vitro models,respectively,to explore the role of RACK1 in mediating PKC-εin early DR.Furthermore,the impact of RACK1 on apoptosis and barrier function of RPE cells was also investigated in the former model.RESULTS Streptozotocin-induced diabetic rats showed increased apoptosis and upregulated expression of RACK1 and PKC-εproteins in RPE cells following a prolonged modeling.Similarly,ARPE-19 cells exposed to high glucose and hypoxia displayed elevated mRNA and protein levels of RACK1 and PKC-ε,accompanied by an increases in ROS production,apoptosis rate,and monolayer permeability.However,silencing RACK1 significantly downregulated the expression of PKC-εand ROS,reduced cell apoptosis and permeability,and protected barrier function.CONCLUSION RACK1 plays a significant role in the development of early DR and might serve as a potential therapeutic target for DR by regulating RPE apoptosis and barrier function.

关键词： Diabetic retinopathy Receptor for activated C kinase 1 Protein kinase C-ε Adult retinal pigment epithelium cell line-19

Dynamic manipulation of multimodal emission in Er3+-activated non-core-shell structure for optical thermometry and information security

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Rare Metals 2024年第4期43卷 1702-1712页

作者： Xuan Liu Zi-Xia lin Yin-Biao Shi xiao-Yan Wang Ming-Ye Ding xiao-Fei yang College of Science Nanjing Forestry University Testing Center Yangzhou University

Regulating luminescent dynamics of lanthanide-based luminescent materials via external stimuli is of great significance in the fields of optical thermometry and high-level anti-counterfeiting.However,it is still a huge challenge to realize multimodal emissions with tunable color outputs from a single activator in simple structures via smart dynamic control of photon transition processes.Herein,we present a mechanistic strategy to achieve multimodal luminescence of Er3+activators with color-switchable outputs in a non-core-shell host.Under the control of excitation dynamics(λex=980,808,1532,377 nm),the population among the intermediate en ergy levels of Er3+and the interaction between Er3+and Yb3+could be precisely modulated through energy transfer and migration processes,leading to the generation of colortunable multimodal luminescence upon diverse excitation modes（non-steady-state,single-/dual-wavelength steady,thermal activation）.Inspired by its special luminescent performance,the as-obtained material exhibits great potential in noncontact thermometry,multimodal anticounterfeiting,and high-capacity information encryption by performing a series of proof-of-concept experiments.Our findings might provide a conceptual model to modulate the luminescent dynamics in a simple-structured system for the generation of color-adjustable multimodal emissions,which is convenient for the development of advanced luminescent materials toward versatile cuttingedge applications.

关键词： Lanthanide ions Multimodal emission Upconversion Downshifting Anti-counterfeiting Luminescent thermometry

Unraveling the Fundamental Mechanism of Interface Conductive Network Influence on the Fast‑Charging Performance of SiO‑Based Anode for Lithium‑Ion Batteries

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Nano-Micro Letters 2024年第3期16卷 53-68页

作者： Ruirui Zhang Zhexi xiao Zhenkang lin Xinghao Yan Ziying He Hairong Jiang Zhou yang Xilai Jia Fei Wei Beijing Key Laboratory of Green Chemical Reaction Engineering and Technology Department of Chemical EngineeringTsinghua UniversityBeijing 100084People’s Republic of China School of Materials Science and Engineering University of Science and Technology BeijingBeijing 100083People’s Republic of China Beijing Key Laboratory of Chemical Power Source and Green Catalysis School of Chemistry and Chemical EngineeringBeijing Institute of TechnologyBeijing 100081People’s Republic of China Institute of Polymer Science and Engineering Department of Chemical EngineeringTsinghua UniversityBeijing 100084People’s Republic of China

Progress in the fast charging of high-capacity silicon monoxide(SiO)-based anode is currently hindered by insufficient conductivity and notable volume expansion.The construction of an interface conductive network effectively addresses the aforementioned problems;however,the impact of its quality on lithium-ion transfer and structure durability is yet to be explored.Herein,the influence of an interface conductive network on ionic transport and mechanical stability under fast charging is explored for the first time.2D modeling simulation and Cryo-transmission electron microscopy precisely reveal the mitigation of interface polarization owing to a higher fraction of conductive inorganic species formation in bilayer solid electrolyte interphase is mainly responsible for a linear decrease in ionic diffusion energy barrier.Furthermore,atomic force microscopy and Raman shift exhibit substantial stress dissipation generated by a complete conductive network,which is critical to the linear reduction of electrode residual stress.This study provides insights into the rational design of optimized interface SiO-based anodes with reinforced fast-charging performance.

关键词： Fast charging SiO anode Interface conductive network Ionic transport Mechanical stability

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Insights into plant salt stress signaling and tolerance

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Journal of Genetics and Genomics 2024年第1期51卷 16-34页

作者： Huapeng Zhou Haifan Shi Yongqing yang Xixian Feng Xi Chen Fei xiao Honghui lin Yan Guo Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education College of Life SciencesSichuan UniversityChengduSichuan 610064China State Key Laboratory of Plant Environmental Resilience China Agricultural UniversityBeijing 100193China College of Grassland Science Nanjing Agricultural UniversityNanjingJiangsu 210095China Xinjiang Key Laboratory of Biological Resources and Genetic Engineering College of Life Science and TechnologyXinjiang UniversityUrumqiXinjiang 830046China

Soil salinization is an essential environmental stressor,threatening agricultural yield and ecological security worldwide.Saline soils accumulate excessive soluble salts which are detrimental to most plants by limiting plant growth and productivity.It is of great necessity for plants to efficiently deal with the adverse effects caused by salt stress for survival and successful reproduction.Multiple determinants of salt tolerance have been identified in plants,and the cellular and physiological mechanisms of plant salt response and adaption have been intensely characterized.Plants respond to salt stress signals and rapidly initiate signaling pathways to re-establish cellular homeostasis with adjusted growth and cellular metabolism.This review summarizes the advances in salt stress perception,signaling,and response in plants.A better under-standing of plant salt resistance will contribute to improving crop performance under saline conditions using multiple engineering approaches.The rhizosphere microbiome-mediated plant salt tolerance as well as chemical priming for enhanced plant salt resistance are also discussed in this review.

关键词： Salt stress Salt perception Salt response and signaling Plant salt tolerance Chemical priming Rhizosphere microbiome

Expression and significance of pigment epithelium-derived factor and vascular endothelial growth factor in colorectal adenoma and cancer

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World Journal of Gastrointestinal Oncology 2024年第3期16卷 670-686页

作者： Ye yang Wu Wen Feng-lin Chen Ying-Jie Zhang xiao-Cong Liu xiao-Yan yang Shan-Shan Hu Ye Jiang Jing Yuan Digestive Diseases Chengdu Qingbaijiang District People's HospitalChengdu 610300Sichuan ProvinceChina Digestive Diseases Chengdu Second People’s HospitalChengdu 610000Sichuan ProvinceChina Graduate School Chengdu Medical CollegeChengdu 610000Sichuan ProvinceChina

BACKGROUND The incidence and mortality of colorectal cancer(CRC)are among the highest in the world,and its occurrence and development are closely related to tumor neovascularization.When the balance between pigment epithelium-derived factors(PEDF)that inhibit angiogenesis and vascular endothelial growth factors(VEGF)that stimulate angiogenesis is broken,angiogenesis is out of control,resulting in tumor development.Therefore,it is very necessary to find more therapeutic targets for CRC for early intervention and later treatment.AIM To investigate the expression and significance of PEDF,VEGF,and CD31-stained microvessel density values(CD31-MVD)in normal colorectal mucosa,adenoma,and CRC.METHODS In this case-control study,we collected archived wax blocks of specimens from the Digestive Endoscopy Center and the General Surgery Department of Chengdu Second People's Hospital from April 2022 to October 2022.Fifty cases of specimen wax blocks were selected as normal intestinal mucosa confirmed by electronic colonoscopy and concurrent biopsy(normal control group),50 cases of specimen wax blocks were selected as colorectal adenoma confirmed by electronic colonoscopy and pathological biopsy(adenoma group),and 50 cases of specimen wax blocks were selected as CRC confirmed by postoperative pathological biopsy after inpatient operation of general surgery(CRC group).An immunohistochemical staining experiment was carried out to detect PEDF and VEGF expression in three groups of specimens,analyze their differences,study the relationship between the two and clinicopathological factors in CRC group,record CD31-MVD in the three groups,and analyze the correlation of PEDF,VEGF,and CD31-MVD in the colorectal adenoma group and the CRC group.The F test or adjusted F test is used to analyze measurement data statistically.Kruskal-Wallis rank sum test was used between groups for ranked data.The chi-square test,adjusted chi-square test,or Fisher's exact test were used to compare the rates between groups.All differences between groups were co

关键词： Pigment epithelium-derived factors Vascular endothelial growth factor Microvessel density Colorectal adenoma Colorectal cancer Targeted therapy