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Identification of differentially expressed mRNAs as novel predictive biomarkers for gastric cancer diagnosis and prognosis

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World Journal of Gastrointestinal Oncology 2024年第5期16卷 1947-1964页

作者： Jian-Wei Zhou Yi-Bing Zhang Zhi-Yang huang Yu-ping yuan Jie Jin Department of Gastroenterology Wenzhou Central HospitalDingli Clinical College of Wenzhou Medical UniversityThe Second Affiliated Hospital of Shanghai UniversityWenzhou 325000Zhejiang ProvinceChina

BACKGROUND Gastric cancer(GC)has a high mortality rate worldwide.Despite significant progress in GC diagnosis and treatment,the prognosis for affected patients still remains unfavorable.AIM To identify important candidate genes related to the development of GC and iden-tify potential pathogenic mechanisms through comprehensive bioinformatics analysis.METHODS The Gene Expression Omnibus database was used to obtain the GSE183136 dataset,which includes a total of 135 GC samples.The limma package in R software was employed to identify differentially expressed genes(DEGs).Thereafter,enrichment analyses of Gene Ontology(GO)terms and Kyoto Encyclopedia of Genes and Genomes(KEGG)pathways were performed for the gene modules using the clusterProfile package in R software.The protein-protein interaction(PPI)networks of target genes were constructed using STRING and visualized by Cytoscape software.The common hub genes that emerged in the cohort of DEGs that was retrieved from the GEPIA database were then screened using a Venn Diagram.The expression levels of these overlapping genes in stomach adenocarcinoma samples and non-tumor samples and their association with prognosis in GC patients were also obtained from the GEPIA database and Kaplan-Meier curves.Moreover,real-time quantitative polymerase chain reaction(RT-qPCR)and western blotting were performed to determine the mRNA and protein levels of glutamic-pyruvic transaminase(GPT)in GC and normal immortalized cell lines.In addition,cell viability,cell cycle distribution,migration and invasion were evaluated by cell counting kit-8,flow cytometry and transwell assays.Furthermore,we also conducted a retrospective analysis on 70 GC patients diagnosed and surgically treated in Wenzhou Central Hospital,Dingli Clinical College of Wenzhou Medical University,The Second Affiliated Hospital of Shanghai University between January 2017 to December 2020.The tumor and adjacent normal samples were collected from the patients to determine the potential association between the expression lev

关键词： Gastric cancer Differentially expressed genes Bioinformatics Hub genes Prognosis

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A versatile model with three-dimensional triangular lattice for unconventional transport and various topological effects

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National Science Review 2024年第1期11卷 204-214页

作者： Jing-Yang You Gang Su yuan ping Feng Department of Physics National University of Singapore Kavli Institute for Theoretical Sciences and CAS Center for Excellence in Topological Quantum Computation University of Chinese Academy of Sciences Centre for Advanced 2D Materials National University of Singapore

The finite Berry curvature in topological materials can induce many subtle phenomena, such as the anomalous Hall effect(AHE), spin Hall effect(SHE), anomalous Nernst effect(ANE), non-linear Hall effect(NLHE) and bulk photovoltaic effects. To explore these novel physics as well as their connection and coupling, a precise and effective model should be developed. Here, we propose such a versatile model—a 3D triangular lattice with alternating hopping parameters, which can yield various topological phases,including kagome bands, triply degenerate fermions, double Weyl semimetals and so on. We reveal that this special lattice can present unconventional transport due to its unique topological surface states and the aforementioned topological phenomena, such as AHE, ANE, NLHE and the topological photocurrent effect. In addition, we also provide a number of material candidates that have been synthesized experimentally with this lattice, and discuss two materials, including a non-magnetic triangular system for SHE, NLHE and the shift current, and a ferromagnetic triangular lattice for AHE and ANE. Our work provides an excellent platform, including both the model and materials, for the study of Berry-curvature-related physics.

关键词： three-dimensional triangular lattice different topological phases various topological effects Berry curvature

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Superiority of a Convolutional Neural Network Model over Dynamical Models in Predicting Central Pacific ENSO

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Advances in Atmospheric Sciences 2024年第1期41卷 141-154页

作者： Tingyu WANG ping huang Center for Monsoon System Research Institute of Atmospheric PhysicsChinese Academy of SciencesBeijing 100029China Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters(CIC-FEMD) Nanjing University of Information Science&TechnologyNanjing 210044China State Key Laboratory of Numerical Modeling for Atmospheric Sciences and Geophysical Fluid Dynamics Institute of Atmospheric PhysicsChinese Academy of SciencesBeijing 100029China University of Chinese Academy of Sciences Beijing 100049China

The application of deep learning is fast developing in climate prediction,in which El Ni?o–Southern Oscillation(ENSO),as the most dominant disaster-causing climate event,is a key target.Previous studies have shown that deep learning methods possess a certain level of superiority in predicting ENSO indices.The present study develops a deep learning model for predicting the spatial pattern of sea surface temperature anomalies(SSTAs)in the equatorial Pacific by training a convolutional neural network(CNN)model with historical simulations from CMIP6 models.Compared with dynamical models,the CNN model has higher skill in predicting the SSTAs in the equatorial western-central Pacific,but not in the eastern Pacific.The CNN model can successfully capture the small-scale precursors in the initial SSTAs for the development of central Pacific ENSO to distinguish the spatial mode up to a lead time of seven months.A fusion model combining the predictions of the CNN model and the dynamical models achieves higher skill than each of them for both central and eastern Pacific ENSO.

关键词： ENSO diversity deep learning ENSO prediction dynamical forecast system

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In situ direct reprogramming of astrocytes to neurons via polypyrimidine tract-binding protein 1 knockdown in a mouse model of ischemic stroke

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Neural Regeneration Research 2024年第10期19卷 2240-2248页

作者： Meng yuan Yao Tang Tianwen huang Lining Ke En huang Key Laboratory of Brain Aging and Neurodegenerative Diseases of Fujian Province Fujian Medical UniversityFuzhouFujian ProvinceChina Department of Human Anatomy School of Basic Medical SciencesFujian Medical UniversityFuzhouFujian ProvinceChina Scientific Research Center School of Basic Medical SciencesFujian Medical UniversityFuzhouFujian ProvinceChina Department of Neurology Fujian Medical University Union HospitalFuzhouFujian ProvinceChina Fujian Key Laboratory of Vascular Aging Fujian Medical UniversityFuzhouFujian ProvinceChina

In situ direct reprogramming technology can directly convert endogenous glial cells into functional neurons in vivo for central nervous system repair. Polypyrimidine tract-binding protein 1(PTB) knockdown has been shown to reprogram astrocytes to functional neurons in situ. In this study, we used AAV-PHP.e B-GFAP-sh PTB to knockdown PTB in a mouse model of ischemic stroke induced by endothelin-1, and investigated the effects of GFAP-sh PTB-mediated direct reprogramming to neurons. Our results showed that in the mouse model of ischemic stroke, PTB knockdown effectively reprogrammed GFAP-positive cells to neurons in ischemic foci, restored neural tissue structure, reduced inflammatory response, and improved behavioral function. These findings validate the effectiveness of in situ transdifferentiation of astrocytes, and suggest that the approach may be a promising strategy for stroke treatment.

关键词： astrocyte in situ direct reprogramming ischemic stroke miR-30 based shRNA neuron polypyrimidine tract-binding protein 1 transdifferentiation

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Analysis on the causes of massive stranding of Yellow Sea green tide on Lianyungang and Rizhao coasts in 2022

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Journal of Oceanology and Limnology 2024年第3期42卷 816-830页

作者： Lingjuan WU Juan huang Yi DING Guiyan LIU Shuai huang Song GAO Chao yuan Jiangling XU ping WU Rui huang Ruobing WEN Jie MEI North China Sea Marine Forecasting and Hazard Mitigation Center Ministry of Natural ResourcesQingdao 266061China Shandong Key Laboratory of Marine Ecological Environment and Disaster Prevention and Mitigation Qingdao 266061China National Engineering Laboratory for Integrated Aero-Space-Ground-Ocean Big Data Application Technology Xi’an 710129China East China Sea Marine Forecasting and Hazard Mitigation Center Ministry of Natural ResourcesShanghai 200136China North China Sea Ecological Center Ministry of Natural ResourcesQingdao 266033China

In 2022,Yellow Sea green tide caused by Ulva prolifera reached a historic minimum and the coastal areas of Shandong Peninsula were less affected.However,the largest amount of seaweed biomass has been washed ashore on Lianyungang and Rizhao coasts since 2015.We studied the development pattern of Yellow Sea green tide in 2022,and analyzed the key environmental factors on the growth and drifting,then discussed the possible reasons that resulted in the massive stranding of green tide biomass in Lianyungang and Rizhao.Results show under the combined influence of the east to southeast winds and currents with shoreward anomalies,green tide drifted to the coastal waters between Shandong and Jiangsu provinces and the distribution areas located westward compared with previous years(2008–2021).Floating U.prolifera rafts from the coastal waters of Binhai and Sheyang drifted continuously into the coastal waters of Lianyungang and Rizhao,providing important supplements for Yellow Sea green tide.Because green tide in 2022 distributed close to the coastal waters,the abundant nutrients might support their continuous high growth rate.In addition,the amount of rainfall around Shandong Peninsula from late June to early July were significantly higher than in previous years,which might promote the development of green tide to some extent.

关键词： Yellow Sea green tide stranding biomass development pattern environmental factor

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Amphiphilic amino-acid derivatives promote gram-scale single-crystal COFs synthesis

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Science China Chemistry 2024年第2期67卷 415-416页

作者： Yijia yuan Kian ping Loh Department of Chemistry National University of SingaporeSingapore117543Singapore

Covalent organic frameworks(COFs) are crystalline organic compounds synthesized from covalently linked building blocks that extend in space to form a framework structure with periodic pores. The covalent linkages used... 详细信息

关键词： synthesis correction reversible

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Understanding the Low Predictability of the 2015/16 El Niño Event Based on a Deep Learning Model

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Advances in Atmospheric Sciences 2024年第7期41卷 1313-1325页

作者： Tingyu WANG ping huang Xianke YANG Center for Monsoon System Research Institute of Atmospheric PhysicsChinese Academy of SciencesBeijing 100029China National Space Science Center Chinese Academy of SciencesBeijing 100190China State Key Laboratory of Space Weather National Space Science CenterChinese Academy of SciencesBeijing 100190China College of Plant Science and Technology Huazhong Agricultural UniversityWuhan 430070China

The 2015/16 El Niño event ranks among the top three of the last 100 years in terms of intensity,but most dynamical models had a relatively low prediction skill for this event before the summer months.Therefore,the attribution of this particular event can help us to understand the cause of super El Niño–Southern Oscillation events and how to forecast them skillfully.The present study applies attribute methods based on a deep learning model to study the key factors related to the formation of this event.A deep learning model is trained using historical simulations from 21 CMIP6 models to predict the Niño-3.4 index.The integrated gradient method is then used to identify the key signals in the North Pacific that determine the evolution of the Niño-3.4 index.These crucial signals are then masked in the initial conditions to verify their roles in the prediction.In addition to confirming the key signals inducing the super El Niño event revealed in previous attribution studies,we identify the combined contribution of the tropical North Atlantic and the South Pacific oceans to the evolution and intensity of this event,emphasizing the crucial role of the interactions among them and the North Pacific.This approach is also applied to other El Niño events,revealing several new precursor signals.This study suggests that the deep learning method is useful in attributing the key factors inducing extreme tropical climate events.

关键词： ENSO attribution deep learning ENSO prediction extreme El Niño

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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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LH-Nts Neurons Regulate VTA Calcium Dynamics Via Releasing GABA and Nts

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Neuroscience Bulletin 2024年第4期40卷 550-552页

作者： Danni Chen Yinfeng yuan Zhihui huang Yongjie Wang School of Pharmacy Hangzhou Normal UniversityHangzhou311121ZhejiangChina Key Laboratory of Element Class Anti-Cancer Chinese Medicines Engineering Laboratory of Development and Application of Traditional Chinese MedicinesCollaborative Innovation Center of Traditional Chinese Medicines of Zhejiang ProvinceHangzhou Normal UniversityHangzhou311121ZhejiangChina

The peripheral and central nervous systems have numerous examples of two or more neuroactive products co-existing in the same neuron[1],which can simultaneously be released as both fast-acting neurotransmitters and slow-acting regulatory neuropeptides[2].For example,neurons in the lateral hypothalamus(LH)release both irritant neurotensin(Nts)and inhibitory-aminobutyric acid(GABA),two counterproductive substances[3].LH-Nts neurons project to the ventral tegmental area(VTA)and form synaptic connections with dopamine(DA)neurons to regulate reward[4-6].More critically,VTA-DA neurons express the Nts receptor Ntsrl and play a crucial role in cognition,anesthesia,reward,and disgust[4,7,8].Nevertheless,a mechanistic understanding of how stimulation and inhibition work together to control the output of neural circuits remains unclear.It is very difficult to selectively isolate these signaling pathways in cell and circuit-specific manners.

关键词： anesthesia stimulation dopamine

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Influence of calendering process on the structural mechanics and heat transfer characteristics of lithium-ion battery electrodes via DEM simulations

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Particuology 2024年第2期85卷 252-267页

作者： Junpeng Zhang Jingna Sun Huagui huang Zhenge yuan National Engineering Research Center for Equipment and Technology of Cold Strip Rolling Yanshan UniversityQinhuangdao066004China Xingtai Naknor Technology Co. LtdXingtai054000China

Elucidating the intricate correlation between calendering,structure,and performance is crucial to comprehending the relationship between performance parameters and process steps of lithium-ion batteries(LIBs).Discrete element method(DEM)simulations were adopted in this work to calculate the interparticle force and stress tensor under incremental calendering process conditions,which revealed the effect of the anisotropy of complex contact force network on the anisotropy of heat transfer within porous electrode.The thermal conductivity of electrode was predicted using porosity to characterize the process-structure-performance correlation.The comprehensive influence of contact number and con-tact area between particles and current collector determines the magnitude of interfacial thermal resistance and interfacial heat transfer coefficient.For the first time,this work quantitatively analyzed the structural mechanics and heat transfer mechanism during calendering process of porous electrodes,and the results indicate a promising way to optimize and design battery electrode structures.

关键词： Li-ion battery electrode Structural mechanicsAnisotropy Thermal conductivity Discrete element method

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