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Differentially expressed genes in rabbits with traumatic proliferative vitreoretinopathy based on high-throughput sequencing 认领 引用
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作者 Yu-Jie Tang Jiang-Ying Liu +3 位作者 Sheng-Xiang Zhang Bo-Yu Liu Liao Quan Qi-Hua Xu 《International Journal of Ophthalmology(English edition)》 SCIE CAS 2026年第4期665-672,共8页
AIM:To identify differentially expressed genes(DEGs)in rabbits with traumatic proliferative vitreoretinopathy(PVR)using high-throughput sequencing(HTS).METHODS:Thirty-six rabbits were randomly allocated to the control... AIM:To identify differentially expressed genes(DEGs)in rabbits with traumatic proliferative vitreoretinopathy(PVR)using high-throughput sequencing(HTS).METHODS:Thirty-six rabbits were randomly allocated to the control group and the PVR group induced by scleral puncture.On the 28th day following modeling,fundus B-ultrasound and fundus photography were performed on all rabbits,and hematoxylin-eosin(HE)staining was conducted on retinal tissues.RNA sequencing(RNA-Seq)combined with bioinformatics analysis was used to screen PVRassociated DEGs.Gene Ontology(GO)functional enrichment analysis and Kyoto Encyclopedia of Genes and Genomes(KEGG)pathway enrichment analysis were carried out for the identified DEGs.S100A6,EDNRB and CEBPD were randomly selected for quantitative reverse transcription polymerase chain reaction(RT-qPCR)validation to verify the reliability of the RNA-Seq results.RESULTS:Fundus B-ultrasound,fundus photography and retinal HE staining confirmed the successful establishment of the traumatic PVR rabbit model.A total of 1587 DEGs were screened,of which 1094 were significantly up-regulated and 493 were significantly down-regulated.GO function enrichment analysis showed that these DEGs were mainly enriched in immune response,extracellular region and inflammatory response.KEGG pathway enrichment analysis showed that DEGs were mainly involved in the cytokine-cytokine receptor interaction and hematopoietic cell lineage pathway.RT-qPCR results showed that S100A6,CEBPD and EDNRB were significantly increased in PVR group.CONCLUSION:A large number of genes exhibit significant differential expression in rabbits with traumatic PVR,among which S100A6,CEBPD and EDNRB may play an important role in traumatic PVR. 展开更多
关键词 proliferative vitreoretinopathy highthroughput sequencing differentially expressed genes rabbits
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Secure and Differentially Private Edge-Cloud Federated Learning Framework for Privacy-Preserving Maritime AIS Intelligence 认领 引用
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作者 Abuzar Khan Abid Iqbal +3 位作者 Ghassan Husnain Fahad Masood Mohammed Al-Naeem Sajid Iqbal 《Computers, Materials & Continua》 SCIE EI 2026年第6期658-673,共16页
Cloud computing now supports large-scale maritime analytics,yet offloading rich Automatic Identification System(AIS)data to the cloud exposes sensitive operational patterns and complicates compliance with cross-border... Cloud computing now supports large-scale maritime analytics,yet offloading rich Automatic Identification System(AIS)data to the cloud exposes sensitive operational patterns and complicates compliance with cross-border privacy regulations.This work addresses the gap between growing demand for AI-driven vessel intelligence and the limited availability of practical,privacy-preserving cloud solutions.We introduce a privacy-by-design edge-cloud framework in which ports and vessels serve as federated clients,training vessel-type classifiers on local AIS trajectories while transmitting only clipped,Gaussian-perturbed updates to a zero-trust cloud coordinator employing secure and robust aggregation.Using a public AIS corpus with realistic non-IID client partitions,our evaluation shows that non-private FedAvg attains validation AUC≈0.90 and test AUC≈0.78,closely matching a centralized baseline.Moderate differential privacy noise(δ≤0.5)preserves most of this utility across KRUM and trimmed-mean aggregation.Communication analysis indicates that secure aggregation introduces negligible overhead compared with standard FedAvg,while homomorphic encryption increases payload size by roughly an order of magnitude.Membership-inference experiments further demonstrate strong privacy protection,yielding ROC AUC≈0.51 with no correctly inferred training members.Overall,the findings show that effective,regulation-conscious maritime analytics can be achieved without centralizing raw AIS data,offering a practical pathway for deploying resilient,privacy-enhanced AI services in distributed maritime environments. 展开更多
关键词 Federated learning privacy-preserving cloud computing maritime AIS analytics differential privacy
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Differentially Private Data Publishing of Trajectory Synthesis Based on Generalization and Probability 认领 引用
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作者 CAO Wenxin XU Xian 《Journal of Shanghai Jiaotong university(Science)》 EI 2026年第4期1071-1085,I0023,共15页
With the advancement of information technology,the value of data has further emerged.Trajectory data,being a type of massive data,has emerged as a valuable asset in enterprises and a driving force for innovation.Howev... With the advancement of information technology,the value of data has further emerged.Trajectory data,being a type of massive data,has emerged as a valuable asset in enterprises and a driving force for innovation.However,privacy issues are also increasingly prominent.As a result,developing effective methods for protecting the privacy of trajectory data has become a research hotspot.However,most existing methods ignore temporal attributes and spatial distribution characteristics of trajectory data,resulting in loss of important information and reduced efficiency.To improve on the method,a new differentially private trajectory-data publishing algorithm,differentially private trajectory-data publishing based on generalization and probability(TPGP),is proposed in this work.The algorithm has three stages and generates a synthetic trajectory dataset.The first stage pre-processes trajectories,by performing time splitting and Hilbert space partitioning on the compressed trajectory data,without ignoring the time attribute.In the second stage,Laplace noise is added to obtain two key pieces of statistical information:the noisy counts of generalized trajectory and the noisy Markov transition probability with time attribute.The third stage generates and releases synthetic trajectories using the two pieces of statistical information obtained in the second stage.Experimental results indicate that the proposed TPGP scheme has significant advantages over existing methods in terms of ensuring data privacy while improving data utility. 展开更多
关键词 differential privacy trajectory data publishing Laplace mechanism
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PrivLLM-Guard: A Differentially-Private Large Language Model for Real-Time Confidential Medical Text Generation and Summarization 认领 引用
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作者 Ans D.Alghamdi 《Computers, Materials & Continua》 SCIE EI 2026年第6期1687-1727,共41页
How can AI assist doctors in generating clinical reports without compromising patient privacy?This question motivates our development of PrivLLM-Guard,a novel framework for differentially private large language models... How can AI assist doctors in generating clinical reports without compromising patient privacy?This question motivates our development of PrivLLM-Guard,a novel framework for differentially private large language models(LLMs)tailored to real-time confidential medical text generation and summarization.While LLMs have shown promise in automating clinical documentation,the sensitivity of healthcare data demands rigorous privacy protections.PrivLLM-Guard addresses this need by combining advanced—differential privacy techniques with adaptive noise calibration,ensuring robust privacy guarantees without sacrificing utility.The framework integrates bidirectional transformer encoders with autoregressive decoders,further enhanced by privacy-aware attention and gradient perturbation mechanisms.Extensive experiments on three large-scale medical datasets demonstrate BLEU-4 scores of 89.7%for generation and ROUGE-L scores of 92.3%for summarization,while maintaining strict privacy budgets.The model processes 512-token sequences in real time with an average latency of 245 ms and memory usage of just 4.2 GB.Compared to state-of-the-art privacy-preserving LLMs,PrivLLM-Guard improves the utility-privacy trade-off by 15.8%and reduces computational overhead by 23.4%.Key contributions include adaptive noise injection,dynamic privacy budgeting,and an integrated privacy auditing module—collectively advancing secure and trustworthy AI deployment in clinical environments. 展开更多
关键词 Differential privacy large language models medical text generation privacy-preserving computing healthcare AI text summarization real-time processing
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Thermal Assessment of a Differentially Heated Nanofluid-Filled Cavity Containing an Obstacle 认领 引用 被引量：1
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作者 Abdelilah Makaoui El Bachir Lahmer +2 位作者 Jaouad Benhamou Mohammed Amine Moussaoui Ahmed Mezrhab 《Frontiers in Heat and Mass Transfer》 EI CAS 2025年第1期207-230,共24页
This study focuses on numerically investigating thermal behavior within a differentially heated cavity filled with nanofluid with and without obstacles.Numerical comparison with previous studies proves the consistency... This study focuses on numerically investigating thermal behavior within a differentially heated cavity filled with nanofluid with and without obstacles.Numerical comparison with previous studies proves the consistency and efficacy of the lattice Boltzmann method associated with a single relaxation time and its possibility of studying the nanofluid and heat transfer with high accuracy.Key parameters,including nanoparticle type and concentration,Rayleigh number,fluid basis,and obstacle position and dimension,were examined to identify optimal conditions for enhancing heat transfer quality.Principal findings indicated that increasing the Rayleigh number boosts buoyancy forces and alters vortex structure,improving the heat transfer efficiency across all nanofluid configu-rations.Moreover,nanoparticles with higher thermal conductivity,particularly Cu nanoparticles,exhibit slight improvements in heat transfer quality compared to Al2O3 nanoparticles,while higher nanoparticle concentrations generally lead to enhanced heat transfer effectiveness.Water-Cu nanofluids also demonstrate superior heat transfer performance over ethylene glycol-Cu nanofluids.Furthermore,the presence of obstacles at cavity extremities hampers overall heat transfer,whereas those positioned centrally augment heat exchange rates.This research offers valuable insights into optimizing convective heat transfer in nanofluid-filled cavities crucial for various engineering applications. 展开更多
关键词 Nanofluid flow heat transfer quality lattice Boltzmann method nanoparticles differentially heated cavity
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Effects of Mycobacterium vaccae vaccine in a mouse model of tuberculosis: protective action and differentially expressed genes 认领 引用 被引量：12
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作者 Wen-Ping Gong Yan Liang +6 位作者 Yan-Bo Ling Jun-Xian Zhang You-Rong Yang Lan Wang Jie Wang Ying-Chang Shi Xue-Qiong Wu 《Military Medical Research》 SCIE CAS CSCD 2020年第2期125-139,共15页
Background:Tuberculosis is a leading cause of death worldwide.BCG is an effective vaccine,but not widely used in many parts of the world due to a variety of issues.Mycobacterium vaccae(M.vaccae)is another vaccine used... Background:Tuberculosis is a leading cause of death worldwide.BCG is an effective vaccine,but not widely used in many parts of the world due to a variety of issues.Mycobacterium vaccae(M.vaccae)is another vaccine used in human subjects to prevent tuberculosis.In the current study,we investigated the potential mechanisms of M.vaccae vaccination by determining differentially expressed genes in mice infected with M.tuberculosis before and after M.vaccae vaccination.Methods:Three days after exposure to M.tuberculosis H37 Rv strain(5×10~5 CFU),adult BALB/c mice randomly received either M.vaccae vaccine(22.5μg)or vehicle via intramuscular injection(n=8).Booster immunization was conducted 14 and 28 days after the primary immunization.Differentially expressed genes were identified by microarray followed by standard bioinformatics analysis.Results:M.vaccae vaccination provided protection against M.tuberculosis infection(most prominent in the lungs).We identified 2,326 upregulated and 2,221 downregulated genes in vaccinated mice.These changes could be mapped to a total of 123 signaling pathways(68 upregulated and 55 downregulated).Further analysis pinpointed to the MyD88-dependent TLR signaling pathway and PI3 K-Akt signaling pathway as most likely to be functional.Conclusions:M.vaccae vaccine provided good protection in mice against M.tuberculosis infection,via a highly complex set of molecular changes.Our findings may provide clue to guide development of more effective vaccine against tuberculosis. 展开更多
关键词 Mycobacterium tuberculosis Immunotherapeutic effect Immunotherapy Vaccae vaccine Differentially expressed genes Signaling pathway
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AFF1 and AFF4 differentially regulate the osteogenic differentiation of human MSCs 认领 引用 被引量：8
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作者 Chen-chen Zhou Qiu-chan Xiong +7 位作者 Xin-xing Zhu Wen Du Peng Deng Xiao-bing Li Yi-zhou Jiang Shu-juan Zou Cun-yu Wang Quan Yuan 《Bone Research》 SCIE CAS CSCD 2017年第3期207-216,共10页
AFF1 and AFF4 belong to the AFF （AF4/FMR2） family of proteins, which function as scaffolding proteins linking two different transcription elongation factors, positive elongation factor b （P-TEFb） and ELL1/2, in su... AFF1 and AFF4 belong to the AFF （AF4/FMR2） family of proteins, which function as scaffolding proteins linking two different transcription elongation factors, positive elongation factor b （P-TEFb） and ELL1/2, in super elongation complexes （SECs）. Both AFF1 and AFF4 regulate gene transcription through elongation and chromatln remodeling. However, their function in the osteogenic differentiation of mesenchymal stem cells （MSCs） is unknown. In this study, we show that small interfering RNA （siRNA）-mediated depletion of AFF1 in human MSCs leads to increased alkaline phosphatase （ALP） activity, enhanced mineralization and upregulated expression of osteogenic-related genes. On the contrary, depletion of AFF4 significantly inhibits the osteogenic potential of MSCs. In addition, we confirm that overexpression of AFF1 and AFF4 differentially affects osteogenic differentiation in vitro and MSC-mediated bone formation in vivo. Mechanistically, we find that AFFI regulates the expression of DKK1 via binding to its promoter region. Depletion of DKK1 in HA-AFFl-overexpressing MSCs abrogates the impairment of osteogenic differentiation. Moreover, we detect that AFF4 is enriched in the promoter region of ID1. AFF4 knockdown blunts the BRE luciferase activity, SP7 expression and ALP activity induced by BMP2 treatment. In conclusion, our data indicate that AFF1 and AFF4 differentially regulate the osteogenic differentiation of human MSCs.AFF1 and AFF4 belong to the AFF （AF4/FMR2） family of proteins, which function as scaffolding proteins linking two different transcription elongation factors, positive elongation factor b （P-TEFb） and ELL1/2, in super elongation complexes （SECs）. Both AFFI and AFF4 regulate gene transcription through elongation and chromatln remodeling. However, their function in the osteogenic differentiation of mesenchymal stem cells （MSCs） is unknown. In this study, we show that small interfering RNA （siRNA）-mediated depletion of AFF1 in human MSCs leads to increased alkaline phosphatase （ALP） activity, enhanced mineralization and upregulated expression of osteogenic-related genes. On the contrary, depletion of AFF4 significantly inhibits the osteogenic potential of MSCs. In addition, we confirm that overexpression of AFF1 and AFF4 differentially affects osteogenic differentiation in vitro and MSC-mediated bone formation in vivo. Mechanistically, we find that AFFI regulates the expression of DKK1 via binding to its promoter region. Depletion of DKK1 in HA-AFFl-overexpressing MSCs abrogates the impairment of osteogenic differentiation. Moreover, we detect that AFF4 is enriched in the promoter region of ID1. AFF4 knockdown blunts the BRE luciferase activity, SP7 expression and ALP activity induced by BMP2 treatment. In conclusion, our data indicate that AFF1 and AFF4 differentially regulate the osteogenic differentiation of human MSCs. 展开更多
关键词 AFF1 and AFF4 differentially regulate the osteogenic differentiation of human MSCs Figure PCR RT ALP
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Event-Triggered Differentially Private Average Consensus for Multi-agent Network 认领 引用 被引量：18
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作者 Aijuan Wang Xiaofeng Liao Haibo He 《IEEE/CAA Journal of Automatica Sinica》 SCIE EI CSCD 2019年第1期75-83,共9页
This paper investigates the differentially private problem of the average consensus for a class of discrete-time multi-agent network systems(MANSs). Based on the MANSs,a new distributed differentially private consensu... This paper investigates the differentially private problem of the average consensus for a class of discrete-time multi-agent network systems(MANSs). Based on the MANSs,a new distributed differentially private consensus algorithm(DPCA) is developed. To avoid continuous communication between neighboring agents, a kind of intermittent communication strategy depending on an event-triggered function is established in our DPCA. Based on our algorithm, we carry out the detailed analysis including its convergence, its accuracy, its privacy and the trade-off between the accuracy and the privacy level, respectively. It is found that our algorithm preserves the privacy of initial states of all agents in the whole process of consensus computation. The trade-off motivates us to find the best achievable accuracy of our algorithm under the free parameters and the fixed privacy level. Finally, numerical experiment results testify the validity of our theoretical analysis. 展开更多
关键词 Average consensus differentially private event-triggered communication multi-agent network systems (MANSs)
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Bioinformatics analyses of differentially expressed genes associated with spinal cord injury:a microarray-based analysis in a mouse model 认领 引用 被引量：5
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作者 Lei Guo Jing Lv +2 位作者 Yun-Fei Huang Ding-Jun Hao Ji-Jun Liu 《Neural Regeneration Research》 SCIE CAS CSCD 2019年第7期1262-1270,共9页
Gene spectrum analysis has shown that gene expression and signaling pathways change dramatically after spinal cord injury,which may affect the microenvironment of the damaged site.Microarray analysis provides a new op... Gene spectrum analysis has shown that gene expression and signaling pathways change dramatically after spinal cord injury,which may affect the microenvironment of the damaged site.Microarray analysis provides a new opportunity for investigating diagnosis,treatment,and prognosis of spinal cord injury.However,differentially expressed genes are not consistent among studies,and many key genes and signaling pathways have not yet been accurately studied.GSE5296 was retrieved from the Gene Expression Omnibus DataSet.Differentially expressed genes were obtained using R/Bioconductor software(expression changed at least two-fold;P < 0.05).Database for Annotation,Visualization and Integrated Discovery was used for functional annotation of differentially expressed genes and Animal Transcription Factor Database for predicting potential transcription factors.The resulting transcription regulatory protein interaction network was mapped to screen representative genes and investigate their diagnostic and therapeutic value for disease.In total,this study identified 109 genes that were upregulated and 30 that were downregulated at 0.5,4,and 24 hours,and 3,7,and 28 days after spinal cord injury.The number of downregulated genes was smaller than the number of upregulated genes at each time point.Database for Annotation,Visualization and Integrated Discovery analysis found that many inflammation-related pathways were upregulated in injured spinal cord.Additionally,expression levels of these inflammation-related genes were maintained for at least 28 days.Moreover,399 regulation modes and 77 nodes were shown in the protein-protein interaction network of upregulated differentially expressed genes.Among the 10 upregulated differentially expressed genes with the highest degrees of distribution,six genes were transcription factors.Among these transcription factors,ATF3 showed the greatest change.ATF3 was upregulated within 30 minutes,and its expression levels remained high at28 days after spinal cord injury.These key genes screened by bioinformatics tools can be used as biological markers to diagnose diseases and provide a reference for identifying therapeutic targets. 展开更多
关键词 nerve regeneration spinal cord injury differentially expressed genes bioinformatics analyses Database for Annotation,Visualization and Integrated Discovery analysis inflammation Kyoto Encyclopedia of Genes and Genomes pathway microarray transcription factors neural regeneration
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Identification of differentially expressed genes regulated by methylation in colon cancer based on bioinformatics analysis 认领 引用 被引量：8
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作者 Yu Liang Cheng Zhang Dong-Qiu Dai 《World Journal of Gastroenterology》 SCIE CAS 2019年第26期3392-3407,共16页
BACKGROUND DNA methylation, acknowledged as a key modification in the field of epigenetics, regulates gene expression at the transcriptional level. Aberrant methylation in DNA regulatory regions could upregulate oncog... BACKGROUND DNA methylation, acknowledged as a key modification in the field of epigenetics, regulates gene expression at the transcriptional level. Aberrant methylation in DNA regulatory regions could upregulate oncogenes and downregulate tumor suppressor genes without changing the sequences.However, studies of methylation in the control of gene expression are still inadequate. In the present research, we performed bioinformatics analysis to clarify the function of methylation and supply candidate methylation-related biomarkers and drivers for colon cancer.AIM To identify and analyze methylation-regulated differentially expressed genes(MeDEGs) in colon cancer by bioinformatics analysis.METHODS We downloaded RNA expression profiles, Illumina Human Methylation 450 K BeadChip data, and clinical data of colon cancer from The Cancer Genome Atlas project. MeDEGs were identified by analyzing the gene expression and methylation levels using the edgeR and limma package in R software. Gene ontology(GO) and Kyoto Encyclopedia of Genes and Genomes(KEGG) pathway enrichment analyses were performed in the DAVID database and KEGG Orthology-Based Annotation System 3.0, respectively. We then conducted Kaplan–Meier survival analysis to explore the relationship between methylation and expression and prognosis. Gene set enrichment analysis(GSEA) and investigation of protein-protein interactions(PPI) were performed to clarify the function of prognosis-related genes.RESULTS A total of 5 up-regulated and 81 down-regulated genes were identified asMeDEGs. GO and KEGG pathway analyses indicated that MeDEGs were enriched in multiple cancer-related terms. Furthermore, Kaplan–Meier survival analysis showed that the prognosis was negatively associated with the methylation status of glial cell-derived neurotrophic factor(GDNF) and reelin(RELN). In PPI networks, GDNF and RELN interact with neural cell adhesion molecule 1. Besides, GDNF can interact with GDNF family receptor alpha(GFRA1), GFRA2, GFRA3, and RET. RELN can interact with RAFAH1 B1,disabled homolog 1, very low-density lipoprotein receptor, lipoprotein receptorrelated protein 8, and NMDA 2 B. Based on GSEA, hypermethylation of GDNF and RELN were both significantly associated with pathways including "RNA degradation," "ribosome," "mismatch repair," "cell cycle" and "base excision repair."CONCLUSION Aberrant DNA methylation plays an important role in colon cancer progression.MeDEGs that are associated with the overall survival of patients may be potential targets in tumor diagnosis and treatment. 展开更多
关键词 Colon cancer Bioinformatics analysis The Cancer Genome Atlas project DNA methylation Methylation-regulated differentially expressed genes Overall survival
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RNA-seq profiling reveals differentially expressed genes as potential markers for vital reaction in skin contusion:a pilot study 认领 引用 被引量：4
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作者 Jingtao Xu Rui Zhao +7 位作者 Ye Xue Huanqin Xiao Yanliang Sheng Dong Zhao Jietao He Hongyan Huang Qi Wang Huijun Wang 《Forensic Sciences Research》 2018年第2期153-160,共8页
Detection of the vitality of wounds is essential in forensic practice.The present study used Illumina RNA-seq technology to determine gene expression profiles in contused mouse skin.In obtained high quality sequencing... Detection of the vitality of wounds is essential in forensic practice.The present study used Illumina RNA-seq technology to determine gene expression profiles in contused mouse skin.In obtained high quality sequencing reads,the reads were mapped onto a reference transcriptome(Mus_musculus.GRCm38.83).The results revealed that there were 659 upregulated and 996 down-regulated differentially expressed genes(DEGs)in contused mouse skin.The DEGs were further analyzed using the Gene Ontology and the Kyoto Encyclopedia of Genes and Genomes databases.Genes from different functional categories and signalling pathways were enriched,including the immune system process,immune response,defense response,cytokine-cytokine receptor interaction,complement and coagulation cascades and chemokine signalling pathway.Expression patterns of 11 DEGs were verified by RT-qPCR in mice skins.In addition,alterations of five DEGs were also analyzed in postmortem human wound samples.The results were in concordance with the results of RNA-seq.These findings suggest that RNA-seq is a powerful tool to reveal DEGs as potential markers for vital reaction in terms of forensic practices. 展开更多
关键词 Forensic pathology skin contusion vital reaction RNA-seq differentially expressed genes
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Transforming growth factor β1 is a differentially expressed candidate protein of congestive heart failure with Qi-deficiency-blood-stasis syndrome 认领 引用 被引量：4
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作者 Li Xiaoqian Huang Pinxian +2 位作者 Wang Shijun Cao Xuebin He Jiancheng 《Journal of Traditional Chinese Medicine》 SCIE CSCD 2020年第2期311-316,共6页
OBJECTIVE: To investigate the role of tongue coating fluid protein in regulation of congestive heart failure(CHF) in Qi-deficiency-blood-stasis syndrome.METHODS: We studied patients with CHF(3 patients with Qi-deficie... OBJECTIVE: To investigate the role of tongue coating fluid protein in regulation of congestive heart failure(CHF) in Qi-deficiency-blood-stasis syndrome.METHODS: We studied patients with CHF(3 patients with Qi-deficiency-blood-stasis syndrome and 3 without Qi-deficiency-blood-stasis syndrome) to investigate differentially expressed proteins. We also included a control group. A biotin label-based antibody array was used for testing tongue coating fluid samples from patients. Net-work analysis of these differentially expressed proteins was conducted using the STRING database,which can predict the relations between differentially expressed proteins and CHF with Qi-deficiency-blood-stasis syndrome.RESULTS: A total of seven differentially expressed proteins were identified, and among these, transforming growth factor β1(TGF-β1) gets a particular attention for us has drawn specific attention.Network analysis showed a homologous relationship of TGF-β1 with bone morphogenetic protein15, which is associated with myocardial fibrosis.CONCLUSION: Occurrence and development of CHF may result from certain DE-proteins and associated signaling pathways. TGF-β1 protein may be a candidate marker for assessing the risk of CHF in Qideficiency-blood-stasis syndrome. 展开更多
关键词 Congestive heart failure Qi-deficiency blood-stasis Transforming growth factorβ1 Bone morphogenetic protein 15 Differentially expressed protein
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Differentially Expressed Proteins in Rat Hippocampus after Chronic Immobilization Stress and Intervention Using Xiao Yao San Decoction 认领 引用 被引量：3
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作者 Mei-Jing KOU Zhe XUE +3 位作者 Yan-Yun LIU Yue-Yun LIU Yan LIU Jia-Xu CHEN 《Digital Chinese Medicine》 CAS 2018年第3期219-227,共9页
Objective To identify differentially expressed proteins in the hippocampus of rats after chronic immobilization stress(CIS)using a proteomics approach,and to study the effect of the Xiao Yao San(XYS)decoction on diffe... Objective To identify differentially expressed proteins in the hippocampus of rats after chronic immobilization stress(CIS)using a proteomics approach,and to study the effect of the Xiao Yao San(XYS)decoction on differentially expressed proteins.Methods Twenty-four Sprague Dawley rats were randomly assigned to one of four groups of equal body weight:control(non-stress),7-day stress,21-day stress and21-day stress+XYS treatment groups.Two-dimensional gel electrophoresis(2-DE)was used to detect differences in protein expression in rat hippocampus.One differentially expressed protein was measured and verified by western blotting.Results Seventeen proteins showed differential expression.Among these,eight could be identified:glial fibrillary acidic protein-2(GFAP-2),tubulin alpha-1c,cytoplasmic muscle actin2,14-3-3protein,β-2a tubulin,phosphatidylethanolamine binding protein,synucleinαsyn3,and a low molecular weight(18kD)protein.Six of these proteins exhibited increased expression,one showed decreased expression,and the other protein,which comprised five subtypes,were either increased or decreased.These proteins are known to be involved in immunity,signal transduction,cell cycle control,apoptosis,regulation of enzyme activity,cytoskeleton structure,and synaptic plasticity.GFAP-2was further analyzed,and its differential expression confirmed by western blotting.Conclusion Some proteins are differentially expressed in the hippocampus of rats under chronic stress.The biological functions of these differentially expressed proteins are varied.Finally,the XYS decoction can significantly up-or down-regulate these protein expression levels. 展开更多
关键词 Chronic immobilization stress Syndrome of liver-depression and spleen-deficiency Rat Hippocampus XYS decoction Differentially expressed proteins
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A comparative analysis of differentially expressed genes in rostral and caudal regions after spinal cord injury in rats 认领 引用 被引量：1
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作者 Xue-Min Cao Sheng-Long Li +4 位作者 Yu-Qi Cao Ye-Hua Lv Ya-Xian Wang Bin Yu Chun Yao 《Neural Regeneration Research》 SCIE CAS CSCD 2022年第10期2267-2271,共5页
The initial mechanical damage of a spinal cord injury(SCI)triggers a progressive secondary injury cascade,which is a complicated process integrating multiple systems and cells.It is crucial to explore the molecular an... The initial mechanical damage of a spinal cord injury(SCI)triggers a progressive secondary injury cascade,which is a complicated process integrating multiple systems and cells.It is crucial to explore the molecular and biological process alterations that occur after SCI for therapy development.The differences between the rostral and caudal regions around an SCI lesion have received little attention.Here,we analyzed the differentially expressed genes between rostral and caudal sites after injury to determine the biological processes in these two segments after SCI.We identified a set of differentially expressed genes,including Col3a1,Col1a1,Dcn,Fn1,Kcnk3,and Nrg1,between rostral and caudal regions at different time points following SCI.Functional enrichment analysis indicated that these genes were involved in response to mechanical stimulus,blood vessel development,and brain development.We then chose Col3a1,Col1a1,Dcn,Fn1,Kcnk3,and Nrg1 for quantitative real-time PCR and Fn1 for immunostaining validation.Our results indicate alterations in different biological events enriched in the rostral and caudal lesion areas,providing new insights into the pathology of SCI. 展开更多
关键词 biological process caudal differentially expressed genes Gene Ontology hemisection immunostaining Rattus norvegicus RNA-sequencing rostral spinal cord injury
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A 2GHz Low Power Differentially Tuned CMOS Monolithic LC-VCO 认领 引用 被引量：1
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作者 张利 池保勇 +2 位作者 姚金科 王志华 陈弘毅 《Journal of Semiconductors》 CAS 北大核心 2006年第9期1543-1547,共5页
A 2GHz differentially tuned CMOS monolithic LC-VCO is designed and fabricated in a 0.18μm CMOS process. The VCO has a 16.15% tuning range （from 1. 8998 to 2. 2335GHz） through a combination of analog and digital tun... A 2GHz differentially tuned CMOS monolithic LC-VCO is designed and fabricated in a 0.18μm CMOS process. The VCO has a 16.15% tuning range （from 1. 8998 to 2. 2335GHz） through a combination of analog and digital tuning techniques （4-bit binary switch-capacitor array）. The measured phase noise is - 118.17dBc/Hz at a 1MHz offset from a 2. 158GHz carrier. With the presented improved switch,the phase noise varies no more than 3dB at different digital control bits. The phase noise changes only by about 2dB in the tuning range because of the pn-junctions as the varactors. The VCO draws a current of about 2. lmA from a 1.8V power supply and works normally with a 1.5V power supply. 展开更多
关键词 binary switchable-capacitor array CMOS differentially tuned phase noise VCO
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Effects of β-catenin on Differentially Expressed Genes in Multiple Myeloma 认领 引用 被引量：3
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作者 陈辉 柴伟 +7 位作者 李斌 倪明 张国强 刘华玮 张卓 陈继营 周勇刚 王岩 《Journal of Huazhong University of Science and Technology(Medical Sciences)》 2015年第4期546-552,共7页
Summary： This study aimed to identify the differentially expressed genes after silencing of β-catenin in multiple myeloma transduced with β-catenin shRNA. The DNA microarray dataset GSE17385 was downloaded from Gen... Summary： This study aimed to identify the differentially expressed genes after silencing of β-catenin in multiple myeloma transduced with β-catenin shRNA. The DNA microarray dataset GSE17385 was downloaded from Gene Expression Omnibus, including 3 samples of MM1.S （human multiple mye- loma cell lines） cells transduced with control shRNA and 3 samples of MM1.S cells transduced with β-catenin shRNA. Then the differentially expressed genes （DEGs） were screened by using Limma. Their underlying functions were analyzed by employing Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses. Moreover, DEGs annotation was conducted based on the databases of tumor associated genes, tumor suppressed genes and the transcriptional regulation from patterns to profiles. Furthermore, the protein-protein interaction （PPI） relationship was obtained from STRING and the protein-protein interaction network and the functional modules were visual- ized by Cytoscape. Then, the pathway enrichment for the DEGs in the functional module was per- formed. A total of 301 DEGs, including 124 up-regulated and 117 down-regulated DEGs, were screened. Functional enrichment showed that CCNB1 and CDK1 were significantly related to the function of cell proliferation. FOS and JUN were related to innate immune response-activating signal transduction. Pathway enrichment analysis indicated that CCNB 1 and CDK1 were most significantly enriched in the pathway of cell cycle. Besides, FOS and JUN were significantly enriched in the Toll-like receptor signaling pathway. FOXM1 was identified as a transcription factor. Moreover, there existed interactions among CCNB1, FOXM1 and CDK1 in PPI network. The expression of FOS, JUN, CCNB1, FOXM1 and CDK1 may be affected by β-catenin in multiple myeloma. 展开更多
关键词 multiple myeloma β-catenin differentially gene expression fimctional enrichment
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Identification of Differentially Expressed Genes During Ethylene Climacteric of Melon Fruit by Suppression Subtractive Hybridization 认领 引用
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作者 GAO Feng NIU Yi-ding +3 位作者 HAO Jin-feng BADE Rengui ZHANG Li-quan HASIAgula 《Journal of Integrative Agriculture》 SCIE CAS CSCD 2013年第8期1431-1440,共10页
Melon （Cucumis melo L.） is an important horticultural crop worldwide. Ethylene regulates the ripening process and affects the ripening rate. To screen genes that are differentially expressed at the burst of ethylene... Melon （Cucumis melo L.） is an important horticultural crop worldwide. Ethylene regulates the ripening process and affects the ripening rate. To screen genes that are differentially expressed at the burst of ethylene climacteric in melon fruit, we performed suppression subtractive hybridization （SSH） to generate forward and reverse libraries, for which we sequenced 439 and 445 clones, respectively. Our BLAST analysis showed that the genes from the 2 libraries were involved in metabolism, signal transduction, cell structure, transcription, translation, and defense. Six genes were analyzed by qRT-PCR during the differential developmental stage of melon fruit. Our results provide new insight into the understanding of climacteric ripening of melon fruit. 展开更多
关键词 Cucumis melo ethylene climacteric fruit ripening differentially expressed mRNA gene expression suppressionsubtractive hybridization
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Characteristics of Atmospheric Fine Particulate Matter(PM2.5)Induced Differentially Expressed Proteins Determined by Proteomics and Bioinformatics Analyses 认领 引用
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作者 ZHENG Kai CAI Ying +7 位作者 WANG Bing Yu QIN Shuang Jian LI Bo Ru HUANG Hai Yan QIN Xiao Yun LONG Ding Xin ZHANG Zhao Hui XU Xin Yun 《Biomedical and Environmental Sciences》 SCIE CAS CSCD 2020年第8期583-592,共10页
Objective To screen the differentially expressed proteins(DEPs)in human bronchial epithelial cells(HBE)treated with atmospheric fine particulate matter(PM2.5).Methods HBE cells were treated with PM2.5 samples from She... Objective To screen the differentially expressed proteins(DEPs)in human bronchial epithelial cells(HBE)treated with atmospheric fine particulate matter(PM2.5).Methods HBE cells were treated with PM2.5 samples from Shenzhen and Taiyuan for 24 h.To detect overall protein expression,the Q Exactive mass spectrometer was used.Gene ontology(GO),Kyoto encyclopedia of genes and genomes(KEGG),and Perseus software were used to screen DEPs.Results Overall,67 DEPs were screened in the Shenzhen sample-treated group,of which 46 were upregulated and 21 were downregulated.In total,252 DEPs were screened in the Taiyuan sampletreated group,of which 134 were upregulated and 118 were downregulated.KEGG analysis demonstrated that DEPs were mainly enriched in ubiquitin-mediated proteolysis and HIF-1 signal pathways in Shenzhen PM2.5 samples-treated group.The GO analysis demonstrated that Shenzhen sample-induced DEPs were mainly involved in the biological process for absorption of various metal ions and cell components.The Taiyuan PM2.5-induced DEPs were mainly involved in biological processes of protein aggregation regulation and molecular function of oxidase activity.Additionally,three important DEPs,including ANXA2,DIABLO,and AIMP1,were screened.Conclusion Our findings provide a valuable basis for further evaluation of PM2.5-associated carcinogenesis. 展开更多
关键词 PM2.5 Proteomics Bioinformatics Differentially expressed proteins Weighted correlation network analysis
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Identification of differentially expressed mRNAs as novel predictive biomarkers for gastric cancer diagnosis and prognosis 认领 引用
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作者 Jian-Wei Zhou Yi-Bing Zhang +2 位作者 Zhi-Yang Huang Yu-Ping Yuan Jie Jin 《World Journal of Gastrointestinal Oncology》 SCIE 2024年第5期1947-1964,共18页
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 candi... 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 level of GPT and the clinical as well as pathological features of GC patients.RESULTS We selected 19214 genes from the GSE183136 dataset,among which there were 250 downregulated genes and 401 upregulated genes in the tumor samples of stage III-IV in comparison to those in tumor samples of stage I-II with a P-value<0.05.In addition,GO and KEGG results revealed that the various upregulated DEGs were mainly enriched in plasma membrane and neuroactive ligand-receptor interaction,whereas the downregulated DEGs were primarily enriched in cytosol and pancreatic secretion,vascular smooth muscle contraction and biosynthesis of the different cofactors.Furthermore,PPI networks were constructed based on the various upregulated and downregulated genes,and there were a total 15 upregulated and 10 downregulated hub genes.After a comprehensive analysis,several hub genes,including runt-related transcription factor 2(RUNX2),salmonella pathogenicity island 1(SPI1),lysyl oxidase(LOX),fibrillin 1(FBN1)and GPT,displayed prognostic values.Interestingly,it was observed that GPT was downregulated in GC cells and its upregulation could suppress the malignant phenotypes of GC cells.Furthermore,the expression level of GPT was found to be associated with age,lymph node metastasis,pathological staging and distant metastasis(P<0.05).CONCLUSION RUNX2,SPI1,LOX,FBN1 and GPT were identified key hub genes in GC by bioinformatics analysis.GPT was significantly associated with the prognosis of GC,and its upregulation can effectively inhibit the proliferative,migrative and invasive capabilities of GC cells. 展开更多
关键词 Gastric cancer Differentially expressed genes Bioinformatics Hub genes Prognosis
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Analysis of differentially expressed genes in Verruca vulgaris vs.adjacent normal skin by RNA-sequencing 认领 引用
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作者 QINGQING GUO JIAYUE QI +4 位作者 XIAOQIANG LIANG ZIGANG ZHAO JIA BAI FANG XIE CHENGXIN LI 《BIOCELL》 SCIE 2023年第11期2435-2443,共9页
Introduction:Verruca vulgaris is one of the most common low-risk HPV infections and is characterized by excessive proliferation of keratinocytes.Currently,very little genetic information is available regarding verruca... Introduction:Verruca vulgaris is one of the most common low-risk HPV infections and is characterized by excessive proliferation of keratinocytes.Currently,very little genetic information is available regarding verruca vulgaris in the Chinese population.This study aimed to obtain comprehensive transcript information of verruca vulgaris by RNA sequencing.Methods:High-throughput sequencing was performed on three fresh verruca vulgaris samples and adjacent normal skin on the Illumina sequencing platform.The transcriptomes were analyzed using bioinformatics and the differentially expressed genes(DEGs)were verified by immunohistochemistry.Verruca vulgaris exhibited a unique molecular signature.Results:In total,1,643 DEGs were identified in verruca vulgaris compared to normal skin.The functions of the DEGs were studies by Gene Ontology(GO)enrichment,Kyoto Encyclopedia of Genes and Genomes(KEGG)pathway analysis,DEGs Reactome analysis,disease annotation function,and STRING protein-protein interaction(PPI)network analysis.The results revealed 595 GO terms associated with the cell cycle,signal transduction,immune system,signaling molecules,and interaction.The Reactome analysis revealed enrichment in reversible hydration of carbon dioxide and BMP signaling,while the disease annotation function revealed that the enriched DEGs are involved in keratosis disorders.The STRING PPI network showed that the edges with the highest density mainly included the 2′-5′oligoadenylate synthase(OAS)family-related proteins.Furthermore,the M-code analysis found ISG15,IRF7,and OASL were scored as significant modules and their high expression compared to the control was verified by immunohistochemistry.Conclusion:These findings contribute to the genetic information of verruca vulgaris in the Chinese population,revealing that interferon-stimulated genes may play essential roles in verruca vulgaris. 展开更多
关键词 Differentially expressed genes RNA-seq Transcriptome Verruca vulgaris Interferon-stimulated genes
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