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A cell marker-based clustering strategy(cmCluster)for precise cell type identification of scRNA-seq data

Quantitative Biology 2023年第2期11卷 163-174页

作者： Yuwei Huang Huidan Chang Xiaoyi Chen jiayue meng mengyao Han Tao Huang Liyun Yuan Guoqing Zhang CAS Key Laboratory of Computational Biology Bio-Med Big Data CenterShanghai Institute of Nutrition and HealthUniversity of Chinese Academy of SciencesChinese Academy of ScienceShanghai 200031China Ningbo Institute of Life and Health Industry University of Chinese Academy of SciencesNingbo 315000China

Background:The precise and efficient analysis of single-cell transcriptome data provides powerful support for studying the diversity of cell functions at the single-cell *** most important and challenging steps are cell clustering and recognition of cell *** the precision of clustering and annotation are considered separately in most current studies,it is worth attempting to develop an extensive and flexible strategy to balance clustering accuracy and biological explanation ***:The cell marker-based clustering strategy(cmCluster),which is a modified Louvain clustering method,aims to search the optimal clusters through genetic algorithm(GA)and grid search based on the cell type annotation ***:By applying cmCluster on a set of single-cell transcriptome data,the results showed that it was beneficial for the recognition of cell populations and explanation of biological function even on the occasion of incomplete cell type information or multiple data *** addition,cmCluster also produced clear boundaries and appropriate subtypes with potential marker *** relevant code is available in GitHub website(huangyuwei301/cmCluster).Conclusions:We speculate that cmCluster provides researchers effective screening strategies to improve the accuracy of subsequent biological analysis,reduce artificial bias,and facilitate the comparison and analysis of multiple studies.

关键词： single-cell RNA-seq clustering cell markers novel cell types

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Unmodified methodologies in target discovery for small molecule drugs:A rising star

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Chinese Chemical Letters 2022年第12期33卷 4980-4988页

作者： jiayue Tang meng Ou Qiuling Zheng Ya Ding Key Laboratory of Drug Quality Control and Pharmacovigilance Ministry of EducationChina Pharmaceutical UniversityNanjing 210009China State Key Laboratory of Natural Medicines Department of Pharmaceutical AnalysisCollege of PharmacyChina Pharmaceutical UniversityNanjing 210009China

Target discovery,involving target identification and validation,is the prerequisite for drug discovery and *** methodologies and technologies for the precise discovery and confirmation of drug targets are powerful tools in understanding the disease,looking for a drug and elucidating the mechanism of drug *** the common target identification and confirmation methods,the modified method is time-consuming and laborious,which may reduce or change the activity of natural *** unmodified methods developed in recent years without chemical modification have gradually become an important means of studying drug targets.A wide range of unmodified approaches have been reported,introducing and analyzing the recent emerging methodologies and *** review highlights the advantages and limitations of these methods for the application of drug target discovery and presents an overview of their contributions to the target discovery of small molecule *** application and future development trends of methodologies in target discovery are also prospected to provide a reference for drug target research.

关键词： Target discovery Target identification Small molecule drug Methodologies Unmodified

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Flexible ternary carbon black/Bi_(2)Te_(3) based alloy/polylactic acid thermoelectric composites fabricated by additive manufacturing

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Journal of Materiomics 2020年第2期6卷 293-299页

作者： Yong Du Jiageng Chen Qiufeng meng jiayue Xu Biplab Paul Per Eklund School of Materials Science and Engineering Shanghai Institute of Technology100 Haiquan RoadShanghai201418China Thin Film Physics Division Department of PhysicsChemistryand Biology(IFM)Link€oping UniversitySE-58183Link€opingSweden

Flexible ternary carbon black/Bi_(2)Te_(3) based alloy/polylactic acid(CB/BTBA/PLA)composites were fabricated by additive manufacturing and their thermoelectric properties were investigated from 300 K to 360 *** 300 K,as the mass ratios of BTBAs in the composites increased from 38.5% to 71.4%,both the electrical conductivity and Seebeck coefficient of the composites increased from 5.8 S/cm to 13.3 S/cm,and from 60.2 mV/K to 119.9 mV/K,respectively,and the thermal conductivity slightly increased from 0.15 W m^(-1)K^(-1) to 0.25 W m^(-1)K^(-1),as a result,the ZT value of the composites increased from 0.004 to *** the temperature increased from 300 K to 360 K,the electrical conductivity of all the composites slightly decreased,while the thermal conductivity slowly increased,and a highest ZT value of 0.024 was achieved for the composites with 71.4% BTBAs at 320 *** traditional sterolithography,fused deposition modeling,selective laser melting,etc.,this additive manufacturing process can directly print the solutions which contain inorganic fillers and polymer matrixes into almost any designed intricate geometries of thermoelectric composites,therefore this process has great potential to be used for fabrication of flexible polymer based thermoelectric composites and devices.

关键词： Flexible Bi_(2)Te_(3)based alloy Additive manufacturing Thermoelectric

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Microenvironmental effects on growth response of Pinus massoniana to climate at its northern boundary in the Tongbai Mountains,Central China

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Journal of Forestry Research 2024年第1期35卷 44-57页

作者： Jianfeng Peng jiayue Cui Jinbao Li meng Peng Yongtao Ma Xiaoxu Wei Jinkuan Li Xuan Li Yamen Liu Jiaxin Li College of Geography and Environmental Science Henan UniversityKaifeng 475004People’s Republic of China Key Laboratory of Earth System Observation and Simulation of Henan Province Kaifeng 475004People’s Republic of China Department of Geography University of Hong KongHong KongSARPeople’s Republic of China HKU Shenzhen Institute of Research and Innovation Shenzhen 518057People’s Republic of China Henan Academy of Forestry Zhengzhou 450000People’s Republic of China

The Tongbai Mountains is an ecologically sensi-tive region and the northern boundary of Pinus massoniana *** analyze the effect of different microenvironments on tree growth response to climate factors,we developed standard chronologies for earlywood width(EWW),late-wood width(LWW),and total ring width(TRW)of *** at two sampling sites on slopes with different orientations,then analyzed characteristics of the chronolo-gies and their correlations with climate variables from five stations in the region and with a regional normalized differ-ence vegetation index(NDVI).Statistical results showed that the TRW/EWW/LWW chronology consistency and charac-teristics(mean sensitivity,signal to noise ratio,expressed population signal)for trees growing on the southeastern slope were much higher than for trees on the northeastern *** indicated that temperature in current March and August has a significant positive effect on TRW/EWW/LWW formation,and the effect on the northeastern slope was weaker than on the southeastern *** to temperature,precipitation has more complicated effects on tree growth,but the effect on the northeastern slope was also generally weaker than on the southeastern ***-wise linear regression analyses showed that temperature in August was the main limiting factor at the two sampling ***,the response of tree growth on the southeast-ern slope as determined by the NDVI is better than on the northeastern slope,and the TRW/EWW/LWW chronologies for the southeastern slope explained over 50%of the total NDVI variances in ***,the results indicate that the difference in the climate response of *** at two sampling sites is clearly caused by differences in the microenvironment,and such differences should be properly considered in future studies of forest dynamics and climate reconstructions.

关键词： Tree-rings Pinus massoniana lamb Microenvironment Radial growth Climate-growth response

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Control of lupus activity during pregnancy via the engagement of IgG sialylation:novel crosstalk between IgG sialylation and pDC functions

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Frontiers of Medicine 2023年第3期17卷 549-561页

作者： You Wang Sihan Lin jiayue Wu meng Jiang Jianhua Lin Yu Zhang Huihua Ding Haibo Zhou Nan Shen Wen Di Department of Obstetrics and Gynaecology Renji HospitalSchool of MedicineShanghai Jiao Tong UniversityShanghai 200127China Shanghai Key Laboratory of Gynaecologic Oncology Shanghai 200127China State Key Laboratory of Oncogenes and Related Genes Shanghai Cancer InstituteRenji HospitalSchool of MedicineShanghai Jiao Tong UniversityShanghai 200127China Shanghai Institute of Rheumatology Renji HospitalSchool of MedicineShanghai Jiao Tong UniversityShanghai 200001China Center for Autoimmune Genomics and Etiology(CAGE) Cincinnati Children’s Hospital Medical CenterCincinnati Ohio 45229USA Department of Pediatrics University of Cincinnati College of MedicineCincinnati Ohio 45267USA

Immunoglobulin(IgG)glycosylation affects the effector functions of IgG in a myriad of biological processes and has been closely associated with numerous autoimmune diseases,including systemic lupus erythematosus(SLE),thus underlining the pathogenic role of glycosylation aberration in *** study aims to explore the relationship between IgG sialylation patterns and lupus *** to that in serum samples from the control cohort,IgG sialylation level was aberrantly downregulated in serum samples from the SLE cohort at four stages(from preconception to the third trimester of pregnancy)and was significantly associated with lupus activity and fetal loss during lupus *** type I interferon signature of pregnant patients with SLE was negatively correlated with the level of IgG *** lack of sialylation dampened the ability of IgG to suppress the functions of plasmacytoid dendritic cells(pDCs).RNA-seq analysis further revealed that the expression of genes associated with the spleen tyrosine kinase(SYK)signaling pathway significantly differed between IgG-and deSia-IgG-treated *** finding was confirmed by the attenuation of the ability to phosphorylate SYK and BLNK in ***,the coculture of pDCs isolated from pregnant patients with SLE with IgG/deSia-IgG demonstrated the sialylation-dependent anti-inflammatory function of *** findings suggested that IgG influences lupus activity through regulating pDCs function via the modulation of the SYK pathway in a sialic acid-dependent manner.

关键词： pregnancy IgG glycome typeⅠinterferon systemic lupus erythematosus

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Causal relationship between circulating vitamin C and 25-hydroxyvitamin D concentrations and common mental disorders-a Mendelian randomization study

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Food Science and Human Wellness 2024年第4期13卷 1877-1885页

作者： Yuanyuan Wang Lirong Dong meng Zhao Shiyu Yin Pan Da Dengfeng Xu Yifei Lu jiayue Xia Niannian Wang Shaokang Wang Guiju Sun Key Laboratory of Environmental Medicine and Engineering of Ministry of Education and Department of Nutrition and Food HygieneSchool of Public HealthSoutheast UniversityNanjing 210009China Department of Integrated Service and Management Jiangsu Provincial Center for Disease Control and PreventionNanjing 210009China

Mental disorders seriously affect people’s health and social *** Mendelian randomization(MR)study was designed to investigate the causal relationship between circulating vitamin C(VC)or 25-hydroxyvitamin D(25(OH)D)levels and mental *** data used for the MR analysis were derived from the summary genome-wide association studies(GWAS)database for VC and 25(OH)D and from the Finn Gen consortium for fourteen mental *** on the inverse variance weighted(IVW)method,we found a potential causal association between circulating VC and anxiety disorders(IVW:OR=1.139,95%CI:1.023-1.269,P=0.018).However,no causal association was found between VC or 25(OH)D and other mental disorders(P>0.05).In the reverse MR analysis,individuals with Alzheimer’s disease was causally associated with higher concentrations of circulating VC(P=0.012),while individuals with anxiety disorders had a negative association between the concentrations of 25(OH)D(P=0.012).However,the current evidence does not support a causal relationship between VC or 25(OH)D and other mental *** addition,there was no causal association between circulating VC and 25(OH)D(P>0.05).Future studies are needed to confirm these findings and to elucidate the mechanisms of potential causality.

关键词： Circulating vitamin C 25-Hydroxyvitamin D Mental disorder Mendelian randomization

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NIR-Ⅱ photothermal therapy for effective tumor eradication enhanced by heterogeneous nanorods with dual catalytic activities

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Nano Research 2022年第5期15卷 4310-4319页

作者： Linghua Zhang Wenjie Wang meng Ou Xiaoxiao Huang Yu Ma jiayue Tang Ting Hou Sheng Zhang Li Yin Huan Chen Yanglong Hou Ya Ding Key Laboratory of Drug Quality Control and Pharmacovigilance Ministry of EducationChina Pharmaceutical UniversityNanjing 210009China Beijing Key Laboratory for Magnetoelectric Materials and Devices Beijing Innovation Center for Engineering Science and Advanced TechnologySchool of Materials Science and EngineeringPeking UniversityBeijing 100871China Department of Biochemistry School of Life Science and TechnologyChina Pharmaceutical UniversityNanjing 210009China

Rational design and exploitation of nanomaterials with superior treatment properties for suitable indications is a way out to relieve cost constraint of therapy and solve the unsatisfactory efficacy for cancer *** this work,we propose a greatly facile approach to produce heterogeneous Pd-Au nanorods(Pd-Au NRs)that solve the current bottleneck problems of photothermal thermal therapy(PTT)as well as completely eliminate tumors in animal models without toxic side *** Pd clusters on both tips of Au NRs offers Pd-Au NRs three novel functions,i.e.,the extension of the absorption into NIR-Ⅱ region,the activation of prodrug of 5-fluorouracil(5-Fu)via the bioorthogonal reaction,and the peroxidase-mimic activity to produce·*** heterogeneous nanorods showed a high and stable photothermal conversion efficiency(52.07%)in a safer NIR-Ⅱ irradiation region(1,064 nm),which not only eliminate most of tumor cells at only one dose of the irradiation for 5 min but also improve the in situ conversion of 5-fluoro-1-propargyluracil and H2O2 into active 5-Fu and·OH to eradicate residual tumors for inhibiting tumor *** dual catalytic activity-synergistic mechanism of PTT demonstrates the importance of material design in solving current bottleneck problem of tumor therapy.

关键词： heterogeneous nanorods Pd-Au photothermal therapy bioorthogonal catalysis peroxidase-mimic activity

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原版《新莱茵报》的语言风格研究——以第1号和第20号德国相关报道为例

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外国语文 2021年第3期37卷 1-8页

作者：唐艋马嘉悦四川外国语大学德语学院重庆400031

本文以《新莱茵报》原版第1号和第20号为基础,对该期德国相关报道中的简讯、评论和通讯性新闻的语言风格进行分析。无论何种篇章类型,《新莱茵报》均尊重新闻事实,同时又敢于表达批判的政治立场;所作评价建立在事实和对事实进行分析的... 详细信息

本文以《新莱茵报》原版第1号和第20号为基础,对该期德国相关报道中的简讯、评论和通讯性新闻的语言风格进行分析。无论何种篇章类型,《新莱茵报》均尊重新闻事实,同时又敢于表达批判的政治立场;所作评价建立在事实和对事实进行分析的基础上,具有较强说服力。另一方面,不同篇章类型无论在篇章结构还是句子结构和词汇选择上都有所不同,既体现出篇章类型的独特风格,又反映出篇章生产者对特定主题的态度。

关键词：《新莱茵报》语言风格马克思恩格斯

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人类学视域下糖尿病足患者疾痛叙事及文化意涵

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中国医学伦理学 2024年第3期37卷 317-323页

作者：施晓瑞张亦农李蒙刘佳月上海大学社会学院上海200444 西安交通大学第一附属医院内分泌代谢科陕西西安710061

糖尿病足是糖尿病患者常见的慢性并发症之一,也是糖尿病患者最常见的住院原因,更是导致糖尿病患者残疾、死亡的主要病因。在疾病发生发展及治疗过程中,患者经历了身体、心理和社会关系的复杂变化,他们对疾病的理解及实践,是一个不断建... 详细信息

糖尿病足是糖尿病患者常见的慢性并发症之一,也是糖尿病患者最常见的住院原因,更是导致糖尿病患者残疾、死亡的主要病因。在疾病发生发展及治疗过程中,患者经历了身体、心理和社会关系的复杂变化,他们对疾病的理解及实践,是一个不断建构和变化的过程,其中蕴含了受病情推进、家庭关系、社会文化和传统以及医患互动等因素影响下的策略性实践。采用调查访谈、参与式观察等田野调查方法,基于医学人类学的研究理念,以糖尿病足患者丰富多变、充满个性的叙事为切入点理解患者独特细致的疾病故事,集中回答糖尿病足患者所经历的疾病观、治疗观、家庭观、社会观、躯体观的变化。意在提供理解这一群体的新视角,并为改善他们的治疗和管理提供有价值的见解,有助于推动糖尿病足患者整体健康和生活质量的提升。

关键词：糖尿病足疾痛叙事患病经历生命遭遇医学人类学

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基于病理组织切片的肺腺癌肿瘤突变负荷预测模型

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中国生物医学工程学报 2023年第6期42卷 698-709页

作者：孟祥福杨子毅杨啸林侯嘉玥辽宁工程技术大学电子与信息工程学院辽宁葫芦岛125000 中国医学科学院基础医学研究所北京协和医学院基础学院北京100005 南京邮电大学通信与信息工程学院南京210023

肺癌是目前死亡率最高的恶性癌症之一,其中非小细胞肺癌(NSCLC)致死率极高。最近医学研究发现,肿瘤突变负荷(TMB)对于癌症的免疫治疗和化疗的疗效具有较好的预测作用,但传统使用基因测序计算TMB的方法存在检测成本高、周期长、样本依赖... 详细信息

肺癌是目前死亡率最高的恶性癌症之一,其中非小细胞肺癌(NSCLC)致死率极高。最近医学研究发现,肿瘤突变负荷(TMB)对于癌症的免疫治疗和化疗的疗效具有较好的预测作用,但传统使用基因测序计算TMB的方法存在检测成本高、周期长、样本依赖度高等缺点。针对上述问题,本研究提出一种混合卷积神经网络和自注意力机制的深度学习模型(FCA-Former)用于预测TMB。该模型以CoAtNet为骨干网络,通过在网络中结合坐标注意力以及融合深度可分离卷积的方式,提高模型的运算速度以及对病理组织切片图像的全局特征提取能力。实验数据采用TCGA数据库中肺腺癌数字病理切片图像数据集,其中高TMB水平的样本271张,低TMB水平的样本66张。实验结果表明,所提方法达到的最高平均曲线下面积(AUC)为98.1%,比现有最好方法RcaNetr提高9.8%。此项研究结果对于NSCLC的预后治疗效果具有较强的指导意义。

关键词：非小细胞肺癌肿瘤突变负荷(TMB) 卷积神经网络

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