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Integrated analysis of single-cell and bulk RNA sequencing data reveals immune-related lncRNA-mRNA prognostic signature in triple-negative breast cancer

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Genes & Diseases 2024年第2期11卷 571-574页

作者： Hongying zhao Lei Yu lixia Wang Xiangzhe Yin Kailai Liu Wangyang Liu Shihua Lin Li Wang College of Bioinformatics Science and Technology Harbin Medical UniversityHarbinHeilongjiang 150081China College of Biomedical Information and Engineering Hainan Medical UniversityHaikouHainan 571199China

Triple-negative breast cancer(TNBC)is an aggressive subtype characterized by extensive tumor heterogeneity,with limited treatment options and a poor prognosis.1 We used cell type annotation and trajectory analysis to identify two distinct differentiation states of epithelial cells,while tumor cells predominantly resided on one of these branches.Inferring the malignant state of epithelial cells based on copy number variation,280 tumor cells were eventually identified from epithelial cells.Differential genes between tumor cells and non-tumor cells were mainly enriched in immune-related functions and pathways.

关键词： breast cancer signature

Protective effect of resveratrol on rat cardiomyocyte H9C2 cells injured by hypoxia/reoxygenation by regulating mitochondrial autophagy via PTEN-induced putative kinase protein 1/Parkinson disease protein 2 signaling pathway

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Journal of Traditional Chinese Medicine 2022年第2期42卷 176-186页

作者： zhao lixia SUN Wei BAI Decheng Institute of Integrated Traditional Chinese and Western Medicine School of Basic Medical SciencesLanzhou UniversityLanzhou 730000China School of Nursing Gansu University of Chinese MedicineLanzhou 730000China Key Laboratory of Dunhuang Medicine Ministry of EducationGansu University of Chinese MedicineLanzhou 730000China Cardiac Surgery the First Hospital of Lanzhou UniversityLanzhouGansu 730000China

OBJECTIVE:To investigate the protective effect of resveratrol on cardiomyocytes after hypoxia/reoxygenation intervention based on PTEN-induced putative kinase protein 1/Parkinson disease protein 2(PINK1/PARKIN)signaling pathway.METHODS:3-(4,5-Dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide was used to detect the effect of resveratrol on the viability of H9C2 cells;the hypoxia/reoxygenation(H/R)model was established in tri-gas incubator;2’,7’-Dichlorofluorescin diacetate staining was used to measure the content of reactive oxygen species(ROS);the changes of mitochondrial membrane potential was determined by 5,5’,6,6’-Tetrachloro-1,1’,3,3’-tetraethyl-imidacarbocyanine iodide staining;the changes of mitochondrial respiratory chain complex activity was evaluated by enzyme activity kits;flow cytometry was used to detect the ratio of apoptotic cells;transmission electron microscope was used to observe the ultrastructure of H9C2 cells;Western blot was used to detect the protein changes of mitochondrial 20 k Da outer membrane protein(TOM20),translocase of inner mitochondrial membrane 23(TIM23),presenilins associated rhomboid-like protein(PARL),PINK1,PARKIN and mitofusin 1(Mfn1),mitofusin 2(Mfn2),phosphotyrosine independent ligand for the Lck SH2 domain of 62 k Da(P62),microtubule-associated protein 1 light chain 3 beta(LC3B);the m RNA levels of PINK1 and PARKIN was detected by quantitative polymerase chain reaction;immunoprecipitation assay was used to detect the interaction between PARKIN and Ubiquitin.RESULTS:Resveratrol could inhibit the proliferation of H9C2 cells in a time-and concentration-dependent manner;however,pretreatment with low cytotoxic resveratrol could reduce the H/R-induced increase in cellular ROS levels,alleviate the loss of mitochondrial membrane potential induced by H/R,inhibit H/R-induced apoptosis of H9C2 cells,and protect the mitochondrial structure and respiratory chain of H9C2 cells from H/R damage.Resveratrol could further increase the levels of p62,PINK1,PARKIN protein,the expression of

关键词： resveratrol myocytes cardiac hypoxia PTEN phosphohydrolase Parkinson disease associated proteins mitochondrial autophagy

Preface to the Special Issue on Causes, Impacts, and Predictability of Droughts for the Past, Present, and Future

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Advances in Atmospheric Sciences 2024年第2期41卷 191-192页

作者： Tianbao zhao Aiguo DAI Jianping HUANG lixia ZHANG Key Laboratory of Regional Climate-Environment Research for Temperate East Asia Institute of Atmospheric Physics(IAP)Chinese Academy of Sciences(CAS)Beijing 100029China Department of Atmospheric and Environmental Sciences University at AlbanySUNYAlbanyNew York 80307USA Key Laboratory for Semi-Arid Climate Change of the Ministry of Education Lanzhou UniversityLanzhou 730000China State Key Laboratory of Numerical Modeling for Atmospheric Sciences and Geophysical Fluid Dynamics(LASG) Institute of Atmospheric PhysicsChinese Academy of SciencesBeijing 100029China

Drought is a recurring dry condition with below-normal precipitation and is often associated with warm temperatures or heatwaves. A drought event can develop slowly over several weeks or suddenly within days, commonly under abnormal atmospheric conditions(e.g., quasi-stationary high-pressure systems), and can persist for weeks, months, or even years.

关键词： drought within suddenly

Incorporation of source contributions to improve the accuracy of soil heavy metal mapping using small sample sizes at a county scale

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Pedosphere 2024年第1期34卷 170-180页

作者： Jie SONG Xin WANG Dongsheng YU Jiangang LI Yanhe zhao Siwei WANG lixia MA State Key Laboratory of Soil and Sustainable Agriculture Institute of Soil ScienceChinese Academy of SciencesNanjing 210008China Chinese Academy of Sciences University Beijing 100049China Agricultural and Rural Bureau of Luanping County Luanping 068250China

Estimating heavy metal(HM) distribution with high precision is the key to effectively preventing Chinese medicinal plants from being polluted by the native soil. A total of 44 surface soil samples were gathered to detect the concentrations of eight HMs(As, Hg, Cu, Cr, Ni, Zn, Pb, and Cd) in the herb growing area of Luanping County, northeastern Hebei Province, China. An absolute principal component score-multiple linear regression(APCS-MLR) model was used to quantify pollution source contributions to soil HMs. Furthermore, the source contribution rates and environmental data of each sampling point were simultaneously incorporated into a stepwise linear regression model to identify the crucial indicators for predicting soil HM spatial distributions. Results showed that 88% of Cu, 72% of Cr, and 72% of Ni came from natural sources;50% of Zn, 49% of Pb, and 59% of Cd were mainly caused by agricultural activities;and 44% of As and 56% of Hg originated from industrial activities. When three-type(natural, agricultural, and industrial) source contribution rates and environmental data were simultaneously incorporated into the stepwise linear regression model, the fitting accuracy was significantly improved and the model could explain 31%–86% of the total variance in soil HM concentrations. This study introduced three-type source contributions of each sampling point based on APCS-MLR analysis as new covariates to improve soil HM estimation precision, thus providing a new approach for predicting the spatial distribution of HMs using small sample sizes at the county scale.

关键词： absolute principal component score-multiple linear regression Chinese herbal medicine influencing factors spatial distribution stepwise multiple regression

Mapping soil organic matter in cultivated land based on multi-year composite images on monthly time scales

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Journal of Integrative Agriculture 2024年第4期23卷 1393-1408页

作者： Jie Song Dongsheng Yu Siwei Wang Yanhe zhao Xin Wang lixia Ma Jiangang Li State Key Laboratory of Soil and Sustainable Agriculture Institute of Soil ScienceChinese Academy of SciencesNanjing 210008China Agricultural and Rural Bureau of Luanping County Luanping 068250China Chinese Academy of Sciences University Beijing 100049China

Rapid and accurate acquisition of soil organic matter(SOM)information in cultivated land is important for sustainable agricultural development and carbon balance management.This study proposed a novel approach to predict SOM with high accuracy using multiyear synthetic remote sensing variables on a monthly scale.We obtained 12 monthly synthetic Sentinel-2 images covering the study area from 2016 to 2021 through the Google Earth Engine(GEE)platform,and reflectance bands and vegetation indices were extracted from these composite images.Then the random forest(RF),support vector machine(SVM)and gradient boosting regression tree(GBRT)models were tested to investigate the difference in SOM prediction accuracy under different combinations of monthly synthetic variables.Results showed that firstly,all monthly synthetic spectral bands of Sentinel-2 showed a significant correlation with SOM(P<0.05)for the months of January,March,April,October,and November.Secondly,in terms of single-monthly composite variables,the prediction accuracy was relatively poor,with the highest R^(2)value of 0.36 being observed in January.When monthly synthetic environmental variables were grouped in accordance with the four quarters of the year,the first quarter and the fourth quarter showed good performance,and any combination of three quarters was similar in estimation accuracy.The overall best performance was observed when all monthly synthetic variables were incorporated into the models.Thirdly,among the three models compared,the RF model was consistently more accurate than the SVM and GBRT models,achieving an R^(2)value of 0.56.Except for band 12 in December,the importance of the remaining bands did not exhibit significant differences.This research offers a new attempt to map SOM with high accuracy and fine spatial resolution based on monthly synthetic Sentinel-2 images.

关键词： soil organic matter Sentinel-2 monthly synthetic images machine learning model spatial prediction

MoO_(x) nanoclusters on Mo-doped TiO_(2) nanosheets with enhanced singlet oxygen generation and sulfide conversion abilities for photocatalytic aerobic oxidative desulfurization

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Science China Chemistry 2024年第1期67卷 408-414页

作者： Suting Xie Xinyu zhao Dongxiao Wang Huawei Yang lixia Yang Liangjiu Bai Donglei Wei Wenxiang Wang Ying Liang Hou Chen Shaojun Guo College of Chemistry and Materials Science Ludong UniversityYantai 264025China College of Materials Science and Engineering Peking UniversityBeijing 100871China

Photocatalytic aerobic oxidation desulfurization(PAODS)is a promising and sustainable alternative to conventional,energyintensive desulfurization techniques for petroleum products.However,its development is greatly plagued by the low capability in generating highly reactive oxygen species and sluggish kinetics of sulfide oxidation of reported photocatalysts.Here we report a class of MoO_(x)nanocluster decorated on ultrathin Mo-doped TiO_(2)nanosheet(MoO_(x)/MoTiO)catalyst for efficiently facilitating the photocatalytic aerobic oxidation of sulfides.We demonstrate that MoO_(x)/MoTiO can not only promote the generation of highly reactive singlet oxygen(^(1)O_(2))but also enhance the aerobic conversion of sulfides,which leads to a record dibenzothiophene oxidation activity of 3.90 mmol g^(-1)h^(-1).The multiple experimental characterizations and density functional theory calculations collectively reveal that the doped-Mo sites can interact with the photogenerated excitons,enabling directly energy transfer generation of^(1)O_(2)through a new exciton modulation mechanism,and the coordination unsaturated MoO_(x)clusters play the role of co-catalyst to enhance the separation of charge carriers,and effectively catalyze the reaction between sulfides and1O_(2)to form sulfones.

关键词： titanium dioxide photocatalytic aerobic oxidation desulfurization dibenzothiophene singlet oxygen

Potentilla anserina polysaccharide alleviates cadmium-induced oxidative stress and apoptosis of H9c2 cells by regulating the MG53-mediated RISK pathway

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Chinese Journal of Natural Medicines 2023年第4期21卷 279-291页

作者： zhao lixia CHENG Ju LIU Di GONG Hongxia BAI Decheng SUN Wei Institute of Integrated Traditional Chinese and Western Medicine School of Basic Medical SciencesLanzhou UniversityLanzhou 730000China School of Nursing Gansu University of Chinese MedicineLanzhou 730000China Key Laboratory of Dunhuang Medicine Ministry of EducationGansu University of Chinese MedicineLanzhou 730000China Institute of Genetics School of Basic Medical SciencesLanzhou UniversityLanzhou 730000China Key laboratory of Evidence Science Techniques Research and Application of Gansu Province Gansu University of Political Science and LawLanzhou 730000China School of Basic Medical Sciences Gansu University of Chinese MedicineLanzhou 730000China Department of Cardiac Surgery The First Hospital of Lanzhou UniversityLanzhou 730000China

Oxidative stress plays a crucial role in cadmium(Cd)-induced myocardial injury.Mitsugumin 53(MG53)and its mediated reperfusion injury salvage kinase(RISK)pathway have been demonstrated to be closely related to myocardial oxidative damage.Potentilla anserina L.polysaccharide(PAP)is a polysaccharide with antioxidant capacity,which exerts protective effect on Cd-induced damage.However,it remains unknown whether PAP can prevent and treat Cd-induced cardiomyocyte damages.The present study was desgined to explore the effect of PAP on Cd-induced damage in H9c2 cells based on MG53 and the mediated RISK pathway.For in vitro evaluation,cell viability and apoptosis rate were analyzed by CCK-8 assay and flow cytometry,respectively.Furthermore,oxidative stress was assessed by 2',7'-dichlorodihydrofluorescein diacetate(DCFH-DA)staining and using superoxide dismutase(SOD),catalase(CAT),and glutathione/oxidized glutathione(GSH/GSSG)kits.The mitochondrial function was measured by JC-10 staining and ATP detection assay.Western blot was performed to detect the expression of proteins related to MG53,the RISK pathway,and apoptosis.The results indicated that Cd increased the levels of reactive oxygen species(ROS)in H9c2 cells.Cd decreased the activities of SOD and CAT and the ratio of GSH/GSSG,resulting in decreases in cell viability and increases in apoptosis.Interestingly,PAP reversed Cd-induced oxidative stress and cell apoptosis.Meanwhile,Cd reduced the expression of MG53 in H9c2 clls and inhibited the RISK pathway,which was mediated by decreasing the ratio of p-Akt^(Ser473)/Akt,p-GSK3β^(Ser9)/GSK3β and p ERK1/2/ERK1/2.In addition,Cd impaired mitochondrial function,which involved a reduction in ATP content and mitochondrial membrane potential(MMP),and an increase in the ratio of Bax/Bcl-2,cytoplasmic cytochrome c/mitochondrial cytochrome c,and Cleaved-Caspase 3/Pro-Caspase 3.Importantly,PAP alleviated Cd-induced MG53 reduction,activated the RISK pathway,and reduced mitochondrial damage.Interestingly,knockdown of MG53 or inhibition

关键词： Potentilla anserina L. Cadmium MG53 RISK pathway Oxidative stress Apoptosis Polysaccharide

Genetic analysis of transcription factors in dopaminergic neuronal development in Parkinson’s disease

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Chinese Medical Journal 2024年第4期137卷 450-456页

作者： Yuwen zhao lixia Qin Hongxu Pan Tingwei Song Yige Wang Xiaoxia Zhou Yaqin Xiang Jinchen Li Zhenhua Liu Qiying Sun Jifeng Guo Xinxiang Yan Beisha Tang Qian Xu Department of Neurology Xiangya HospitalCentral South UniversityChangshaHunan 410008China Department of Neurology The Second Xiangya HospitalCentral South UniversityChangshaHunan 410011China Bioinformatics Center National Clinical Research Center for Geriatric Disorders Xiangya HospitalCentral South UniversityChangshaHunan 410008China Department of Geriatrics Xiangya HospitalCentral South UniversityChangshaHunan 410008China Centre for Medical Genetics and Hunan Key Laboratory of Medical Genetics School of Life SciencesCentral South UniversityChangshaHunan 410008China Key Laboratory of Hunan Province in Neurodegenerative Disorders Central South UniversityChangshaHunan 410008China

Background:Genetic variants of dopaminergic transcription factor-encoding genes are suggested to be Parkinson’s disease(PD)risk factors;however,no comprehensive analyses of these genes in patients with PD have been undertaken.Therefore,we aimed to genetically analyze 16 dopaminergic transcription factor genes in Chinese patients with PD.Methods:Whole-exome sequencing(WES)was performed using a Chinese cohort comprising 1917 unrelated patients with familial or sporadic early-onset PD and 1652 controls.Additionally,whole-genome sequencing(WGS)was performed using another Chinese cohort comprising 1962 unrelated patients with sporadic late-onset PD and 1279 controls.Results:We detected 308 rare and 208 rare protein-altering variants in the WES and WGS cohorts,respectively.Gene-based association analyses of rare variants suggested that MSX1 is enriched in sporadic late-onset PD.However,the significance did not pass the Bonferroni correction.Meanwhile,72 and 1730 common variants were found in the WES and WGS cohorts,respectively.Unfortunately,single-variant logistic association analyses did not identify significant associations between common variants and PD.Conclusions:Variants of 16 typical dopaminergic transcription factors might not be major genetic risk factors for PD in Chinese patients.However,we highlight the complexity of PD and the need for extensive research elucidating its etiology.

关键词： Parkinson’s disease Transcription factors Dopaminergic neurons Genetic Variants

Puerariae Radix protects against ulcerative colitis in mice by inhibiting NLRP3 inflammasome activation

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Food Science and Human Wellness 2024年第4期13卷 2266-2276页

作者： Yu Ga Yuanyuan Wei Qingyu zhao Yimeng Fan Yannan Zhang Zhifang Zhang Sijia Hao lixia Wang Zhifen Wang Jinlong Han Shuang Wu Zhihui Hao Innovation Centre of Chinese Veterinary Medicine College of Veterinary MedicineChina Agricultural UniversityBeijing 100086China National Center of Technology Innovation for Medicinal Function of Food National Food and Strategic Reserves AdministrationBeijing 100193China Inner Mongolia Medical University Hohhot 010059China China Agricultural University Yantai Institute Yantai 264670China Shandong Academy of Agricultural Sciences Jinan 250100China

Ulcerative colitis(UC)is a common inflammatory disease of the gastrointestinal tract.Traditional Chinese medicine(TCM)has long been used in Asia as a treatment for UC and Puerariae Radix(PR)is a reliable anti-diarrheal therapy.The aims of this study were to investigate the protective effect of PR using the dextran sulfate sodium salt(DSS)-induced UC model in mice and identify molecular mechanisms of PR action.The chemical constituents of PR via ultra-performance liquid chromatography/tandem mass spectrometry and identified potential PR and UC targets using a network pharmacology(NP)approach were obtained to guide mouse experiments.A total of 180 peaks were identified from PR including 48 flavonoids,46 organic acids,14 amino acids,8 phenols,8 carbohydrates,7 alkaloids,6 coumarins and 43 other constituents.NP results showed that caspase-1 was the most dysregulated of the core genes associated with UC.A PR dose of 0.136 mg/g administered to DSS treated mice reversed weight loss and decreased colon lengths found in UC mice.PR also alleviated intestinal mucosal shedding,inflammatory cell infiltration and mucin loss.PR treatment suppressed upregulation of NOD-like receptor protein 3(NLRP3),cysteinyl aspartate-specific proteases-1(caspase-1),apoptosis-associated speck-like(ASC)and gasdermin D(GSDMD)at both the protein and m RNA expression levels.The addition of a small molecule dual-specificity phosphatase inhibitor NSC 95397 inhibited the positive effects of PR.These results indicated that PR exerts a protective effect on DSS-induced colitis by inhibiting NLRP3 inflammasome activation in mice.

关键词： Puerariae Radix Ulcerative colitis Molecular mechanisms Pyroptosis NOD-like receptor protein 3 inflammasome