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Combined ATAC-seq,RNA-seq,and GWAS analysis reveals glycogen metabolism regulatory network in Jinjiang oyster(Crassostrea ariakensis)

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Zoological Research 2024年第1期45卷 201-214页

作者： Biao Wu Xi Chen Jie Hu Zhen-Yuan Wang Yan Wang Da-You Xu Hao-Bing Guo Chang-Wei Shao Li-Qing Zhou xiu-jun sun Tao Yu Xiao-Mei Wang Yan-Xin Zheng Guang-Yi Fan Zhi-Hong Liu State Key Laboratory of Mariculture Biobreeding and Sustainable Goods Yellow Sea Fisheries Research InstituteChinese Academy of Fishery SciencesQingdaoShandong 266071China Laboratory for Marine Fisheries Science and Food Production Processes Laoshan LaboratoryQingdaoShandong 266071China BGI-Qingdao BGI-ShenzhenQingdaoShandong 266426China National Demonstration Center for Experimental Fisheries Science Education Shanghai Ocean UniversityShanghai 201306China Changdao Enhancement and Experiment Station Chinese Academy of Fishery SciencesYantaiShandong 265800China State Key Laboratory of Agricultural Genomics BGI-ShenzhenShenzhenGuangdong 518083China

Glycogen serves as the principal energy reserve for metabolic processes in aquatic shellfish and substantially contributes to the flavor and quality of *** Jinjiang oyster(Crassostrea ariakensis)is an economically and ecologically important species in *** the present study,RNA sequencing(RNA-seq)and assay for transposase-accessible chromatin using sequencing(ATAC-seq)were performed to investigate gene expression and chromatin accessibility variations in oysters with different glycogen *** identified 9483 differentially expressed genes(DEGs)and 7215 genes with significantly differential chromatin accessibility(DCAGs)were obtained,with an overlap of 2600 genes between ***,a significant proportion of these genes were enriched in pathways related to glycogen metabolism,including“Glycogen metabolic process”and“Starch and sucrose metabolism”.In addition,genome-wide association study(GWAS)identified 526 single nucleotide polymorphism(SNP)loci associated with glycogen *** loci corresponded to 241 genes,63 of which were categorized as both DEGs and *** study enriches basic research data and provides insights into the molecular mechanisms underlying the regulation of glycogen metabolism in ***.

关键词： Crassostrea ariakensis Glycogen Transcriptome ATAC GWAS

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Pretreating and normalizing metabolomics data for statistical analysis

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Genes & Diseases 2024年第3期11卷 188-205页

作者： jun sun Yinglin Xia Division of Gastroenterology and Hepatology Department of MedicineDepartment of Microbiology/ImmunologyUIC Cancer CenterUniversity of Illinois ChicagoJesse Brown VA Medical Center Chicago(537)ChicagoIL 60612USA Division of Gastroenterology and Hepatology Department of MedicineUniversity of Illinois ChicagoChicagoIL 60612USA

Metabolomics as a research field and a set of techniques is to study the entire small molecules in biological *** is emerging as a powerful tool generally for pre-cision ***,integration of microbiome and metabolome has revealed the mechanism and functionality of microbiome in human health and ***,metabo-lomics data are very ***/pretreating and normalizing procedures on metabolomics data are usually required before statistical *** this review article,we comprehensively review various methods that are used to preprocess and pretreat metabolo-mics data,including MS-based data and NMR-based data preprocessing,dealing with zero and/or missing values and detecting outliers,data normalization,data centering and scaling,data *** discuss the advantages and limitations of each *** choice for a suitable preprocessing method is determined by the biological hypothesis,the characteristics of the data set,and the selected statistical data analysis *** then provide the perspective of their applications in the microbiome and metabolome research.

关键词： Data centering and scaling Data normalization Data transformation Missing values MS-Baseddata preprocessing NMRData preprocessing Outliers Preprocessing/pretreatment

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Passivity-Based Stabilization for Switched Stochastic Nonlinear Systems

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IEEE/CAA Journal of Automatica Sinica 2024年第5期11卷 1307-1309页

作者： Yaowei sun jun Zhao School of Automation Zhengzhou University of AeronauticsZhengzhou 450046 Henan Key Laboratory of General Aviation Technology Zhengzhou University of AeronauticsZhengzhou 450046China College of Information Science and Engineering Northeastern UniversityShenyang 110819China

Dear Editor,This letter addresses the passivity-based mean square exponential stabilization problem for switched stochastic nonlinear systems.A concept of generalized small-time norm-observability is presented and an appropriate test condition is also *** pre-given passivity rate and average dwell time,a set of feedback controllers is designed by use of the passivity property.

关键词： property letter stabilization

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Metabolites and micronutrition in modulating amyotrophic lateral sclerosis

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Neural Regeneration Research 2024年第6期19卷 1183-1184页

作者： Katerina Claud jun sun Department of Medicine University of Illinois ChicagoChicagoILUSA Jesse Brown VA Medical Center Chicago ChicagoILUSA

Amyotrophic lateral sclerosis(ALS)is a progressive neurodegenerative *** majority of ALS cases are sporadic with only about 20%of familial *** in families with genetic predisposition,there is significant phenotypic va... 详细信息

关键词： sclerosis amyotrophic cases

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Diminishing the Perception Bias in the Working Environment Using a Network Generation-Based Framework

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Tsinghua Science and Technology 2024年第3期29卷 671-683页

作者： jun Qian Tongda Zhang Xiao sun Yueting Chai Department of Automation Tsinghua UniversityBeijing 100084China Department of Mechanical and Energy Engineering Southern University of Science and TechnologyShenzhen 518055Chinaand with Systems Optimization LaboratoryStanford UniversityPalo AltoCA 94305USA

Income inequality is widespread in human society and has important implications for human ***’s perception of the environment bridges income inequality and individual behavioral *** research suggests that social income inequality is usually biased,either overestimated or ***,such phenomena have not been fully explored with quantitive prove,especially in the working environment based on performance data of actual *** fact,the correct perception of people is the basis of a fair environment for their production ***,the perception bias may weaken the adaptability and competitiveness of a company in the *** paper first confirms the prevalence of individual perception bias of income inequality within the working environment based on actual production *** results show that people tend to underestimate income inequity around them,and this underestimation grows with the real unfairness of the working ***,this paper proposes a network generation-based framework with a three-layer structure to correct perception bias using a cooperative network reengineering *** the framework,a homophily-based generative network model is proposed as the key *** simulation results show that our proposed framework effectively reduces individuals’perception bias of income inequality.

关键词： income inequality perception bias Gini coefficient factory production cooperative networkreengineering homophily-based generative network model

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Light(Science & Applications) 2024年第2期13卷 333-346页

作者： Yifan sun Qian Li Ling-jun Kong Xiangdong Zhang Key Laboratory of advanced optoelectronic quantum architecture and measurements of Ministry of Education Beijing Key Laboratory of Nanophotonics&Ultrafine Optoelectronic SystemsSchool of PhysicsBeijing Institute of Technology100081BeijingChina

Compared with electrical neural networks,optical neural networks(ONNs)have the potentials to break the limit of the bandwidth and reduce the consumption of energy,and therefore draw much attention in recent *** far,several types of ONNs have been ***,the current ONNs cannot realize the acceleration as powerful as that indicated by the models like quantum neural *** to construct and realize an ONN with the quantum speedup is a huge ***,we propose theoretically and demonstrate experimentally a new type of optical convolutional neural network by introducing the optical *** is called the correlated optical convolutional neural network(COCNN).We show that the COCNN can exhibit“quantum speedup”in the training *** character is verified from the two *** is the direct illustration of the faster convergence by comparing the loss function curves of the COCNN with that of the traditional convolutional neural network(CNN).Such a result is compatible with the training performance of the recently proposed quantum convolutional neural network(QCNN).The other is the demonstration of the COCNN’s capability to perform the QCNN phase recognition circuit,validating the connection between the COCNN and the ***,we take the COCNN analog to the 3-qubit QCNN phase recognition circuit as an example and perform an experiment to show the soundness and the feasibility of *** results perfectly match the theoretical *** proposal opens up a new avenue for realizing the ONNs with the quantum speedup,which will benefit the information processing in the era of big data.

关键词： process quantum convolution

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Monocyte to High-density Lipoprotein Cholesterol Ratio as a Predictor of Nonalcoholic Fatty Liver Disease in Childhood Obesity

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Current Medical Science 2024年第4期44卷 692-697页

作者： jun-feng ZHANG Feng-qing CAI xiu-cai ZHANG Qing YE Department of Laboratory Medicine Children’s HospitalZhejiang University School of MedicineNational Clinical Research Center for Child HealthHangzhou310052China

Objective Inflammation is involved in the development and progression of nonalcoholic fatty liver disease(NAFLD).The monocyte to high-density lipoprotein cholesterol ratio(MHR)has emerged as a marker for various inflammation-related *** aim of the present study was to investigate the association between the MHR and NAFLD in a population with childhood *** Based on hepatic ultrasound,a total of 504 children with obesity(357 with NAFLD and 147 without NAFLD)were included in the *** correlation between the MHR and NAFLD risk factors was assessed by Pearson’s and Spearman’s *** stepwise logistic regression analyses were conducted to explore the association between the MHR and the risk of *** The MHR in patients with NAFLD was significantly greater than that in patients without NAFLD[0.52(0.44-0.67)versus 0.44(0.34-0.57),P<0.001].Multivariate stepwise logistic regression analysis demonstrated that the MHR[odds ratio(OR):1.033,95%confidence interval(CI):1.015-1.051;P<0.001]was an independent predictor of NAFLD in childhood obesity patients,as were age(OR:1.205,95%CI:1.059-1.371;P=0.005],waist circumference[OR:1.037,95%CI:1.008-1.067;P=0.012],and alanine transaminase[OR:1.067,95%CI:1.045-1.089;P<0.001].Additionally,MHR quartiles showed a significant positive association with the incidence of NAFLD after adjusting for potential confounding *** The present study showed that the MHR may serve as an available and useful indicator of NAFLD in individuals with childhood obesity.

关键词： nonalcoholic fatty liver disease obesity monocyte-to-high-density lipoprotein ratio marker

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A Wideband High-Gain Sawtooth Slot Array Antenna with Frequency-Scanning at Lower Frequency and Fixed-Beam at Higher Frequency

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Chinese Journal of Electronics 2024年第2期33卷 463-471页

作者： Qiang sun Yongling BAN jun HU School of Electronic Science and Engineering University of Electronic Science and Technology of China

Exploring the multifunctional array antenna suitable for complex communication environment has very important research value. In this paper, a millimeter wave(mm-wave) double longitudinal sawtooth slot array antenna(DLSA) based on substrate integrated waveguide(SIW) technology is proposed, which has wideband, highgain and novel beam characteristics. Two irregular longitudinal slots are etched on the SIW conductor surface as the radiation structure. To improve the bandwidth of the DLSA, the metallized vias are added at the transition point of the slots to construct multiple resonant frequency points. By adjusting the size of the slots and the position of the metallized vias, the phase constant can be regulated, and the unusual beam characteristics can be obtained. That is to say, in the lower frequency band, the beam pointing angle increases with frequency. In the higher frequency band,the beam pointing angle is maintained at a fixed angle. Finally, to improve the antenna gain, a 16 × 8 DLSA is fabricated, measured and discussed. The proposed antenna has an impedance matching bandwidth close to 9.7 *** 27 to 33 GHz, the beam pointing angle changes from 8° to 29°. From 33 to 37 GHz, the beam pointing angle is fixed at 29°, and the pointing angle error range is ±1°. In addition, the measured maximum gain is 22.9 d Bi at32 GHz.

关键词： Antenna measurements Slot antennas Surface waves Resonant frequency Gain measurement Conductors Frequency measurement

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Unlocking T cell exhaustion:Insights and implications for CAR-T cell therapy

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Acta Pharmaceutica Sinica B 2024年第8期14卷 3416-3431页

作者： Dian Xiong Haijun Yu Zhi-jun sun State Key Laboratory of Oral&Maxillofacial Reconstruction and Regeneration Key Laboratory of Oral Biomedicine Ministry of EducationHubei Key Laboratory of StomatologySchool&Hospital of StomatologyFrontier Science Center for Immunology and MetabolismTaikang Center for Life and Medical ScienceWuhan UniversityWuhan 430079China Department of Radiation and Medical Oncology Hubei Province Cancer Clinical Study CenterHubei Key Laboratory of Tumor Biological BehaviorsZhongnan Hospital of Wuhan UniversityWuhan 430071China

Chimeric antigen receptor T(CAR-T)cell therapy as a form of adoptive cell therapy(ACT)has shown significant promise in cancer treatment,demonstrated by the FDA-approved CAR-T cell therapies targeting CD19 or B cell maturation antigen(BCMA)for hematological malignancies,albeit with moderate outcomes in solid ***,despite these advancements,the efficacy of CAR-T therapy is often compromised by T cell exhaustion,a phenomenon that impedes the persistence and effector function of CAR-T cells,leading to a relapse rate of up to 75%in patients treated with CD19 or CD22 CAR-T cells for hematological *** to overcome CAR-T exhaustion employ state-of-the-art genomic engineering tools and single-cell sequencing *** this review,we provide a comprehensive understanding of the latest mechanistic insights into T cell exhaustion and their implications for the current efforts to optimize CAR-T cell *** insights,combined with lessons learned from benchmarking CAR-T based products in recent clinical trials,aim to address the challenges posed by T cell exhaustion,potentially setting the stage for the development of tailored next-generation approaches to cancer treatment.

关键词： Cancer immunotherapy CAR-T therapy T cell exhaustion Tumor immune microenvironment Spatial immune contexture Single-cell technologies CAR-T engineering Combination therapy

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Survey on performance of vertical slot and nature-like fishways at Angu hydropower station, Southwest China

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Water Science and Engineering 2024年第1期17卷 83-91页

作者： jun-jian sun Jia-yue Shi Qi Zhang Xiao-tao Shi jun-jun Tan PowerChina Huadong Engineering Corporation Limited Hangzhou 311122China Hubei International Science and Technology Cooperation Base of Fish Passage China Three Gorges UniversityYichang 443002China

To restore dam-blocked natural fish migratory passages,a growing number of artificial fishways have been built in water conservancy and hydropower projects in *** Angu hydropower station involved diverse important fish habitats in the lower reaches of the Daduhe River in Southwest ***,a vertical slot fishway(VSF)and a nature-like fishway(NLF)were built near the backwater area of the reservoir to connect the upstream and downstream *** and aquatic ecological surveys were conducted after the completion of the project to estimate the fish passing effect of the two *** results indicated that both fishways were in effective operation and could maintain the desired hydrodynamic conditions and be used by several local fish *** the survey,149 fish from 15 species and 111 fish from 17 species were captured by the traps in the VSF and NLF,respectively,while 1263 fish from 27 species were found in the downstream *** species captured in the VSF were not found in the NLF,and vice versa,which implied the different preferences of ***,3789 signals including 2099 upward ones and 1690 downward ones were monitored with an ultrasonic fish detector at the inlet of the *** findings revealed the characteristics of fish species observed in and near the fishways and provided valuable insights into the different fish passing capabilities of VSFandNLF.

关键词： Vertical slot fishway Nature-like fishway Aguatic ecological survey Fishwaymonitoring Statistical analysis

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