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| 1 | An isoflavone derivative potently inhibits the angiogenesis and progression of triple-negative breast cancer by targeting the MTA2/SerRS/VEGFA pathway显示文摘Objective:Angiogenesis plays a vital role in tumor growth and metastasis.Here,we aimed to find novel efficient antiangiogenic molecules targeting vascular endothelial growth factor A(VEGFA)at the transcriptional level to treat triple-negative breast cancer(TNBC).Methods:We used a cell-based seryl tRNA synthetase(SerRS)promoter-driven dual-luciferase reporter system to screen an in-house library of 384 naturally occurring small molecules and their derivatives to find candidate molecules that could upregulate the expression of SerRS,a potent transcriptional repressor of VEGFA.The levels of SerRS and VEGFA were examined by quantitative RT-PCR(qRT-PCR),western blotting,and/or ELISAs in TNBC cells after candidate molecule administration.Zebrafish,the Matrigel plug angiogenesis assay in mice,the TNBC allograft,and xenograft mouse models were used to evaluate thein vivoanti-angiogenic and anti-cancer activities.Furthermore,the potential direct targets of the candidates were identified by proteomics and biochemical studies.Results:We found the most active compound was 3-(4-methoxyphenyl)quinolin-4(1H)-one(MEQ),an isoflavone derivative.In TNBC cells,MEQ treatment resulted in increased SerRS mRNA(P<0.001)and protein levels and downregulated VEGFA production.Both the vascular development of zebrafish and Matrigel plug angiogenesis in mice were inhibited by MEQ.MEQ also suppressed the angiogenesis in TNBC allografts and xenografts in mice,resulting in inhibited tumor growth and prolonged overall survival(P<0.05).Finally,we found that MEQ regulated SerRS transcription by interacting with MTA2(Metastasis Associated 1 Family Member 2).Conclusions:Our findings suggested that the MTA2/SerRS/VEGFA axis is a drug-treatable anti-angiogenic target,and MEQ is a promising anti-tumor molecule that merits further investigation for clinical applications. | Xiaotong Zhang Gengyi Zou Xiyang Li Lun Wang Tianyu Xie Jin Zhao Longlong Wang Shunchang Jiao Rong Xiang Haoyu Ye Yi Shi | 2020 | Cancer Biology & Medicine2020，17，3： | 6 |
| 2 | A nanocleaner specifically penetrates the blood-brain barrier at lesions to clean toxic proteins and regulate inflammation in Alzheimer's disease显示文摘Insurmountable blood-brain barrier(BBB) and complex pathological features are the key factors affecting the treatment of Alzheimer's disease(AD).Poor accumulation of drugs in lesion sites and undesired effectiveness of simply reducing Aβ deposition or TAU protein need to be resolved urgently.Herein,a nanocleaner is designed with a rapamycin-loaded ROS-responsive PLGA core and surface modification with KLVFF peptide and acid-cleavable DAG peptide [R@(ox-PLGA)-KcD].DAG can enhance the targeting and internalization effect of nanocleaner towards neurovascular unit endothelial cells in AD lesions,and subsequently detach from nanocleaner in response to acidic microenvironment of endosomes to promote the transcytosis of nanocleaner from endothelial cells into brain parenchyma.Then exposed KLVFF can capture and carry Aβ to microglia,attenuating Aβ-induced neurotoxicity.Strikingly,rapamycin,an autophagy promoter,is rapidly liberated from nanocleaner in the high ROS level of lesions to improve Aβ degradation and normalize inflammatory condition.This design altogether accelerates Aβ degradation and alleviates oxidative stress and excessive inflammatory response.Collectively,our finding offers a strategy to target the AD lesions precisely and multi-pronged therapies for clearing the toxic proteins and modulating lesion microenvironment,to achieve efficient AD therapy. | Ting Lei Zhihang Yang Xue Xia Yuxiu Chen Xiaotong Yang Rou Xie Fan Tong Xiaolin Wang Huile Gao | 2021 | Acta Pharmaceutica Sinica B2021，11，12： | 4 |
| 3 | UPLC-MS metabolomics provides insights into the diff erences between black- and white-shelled Pacifi c oysters Crassostrea gigas显示文摘A variety of shell colors are one of the most fundamental characteristics of molluscs,which have importantly ecological and economic signifi cance.The Pacifi c oyster Crassostrea gigas is distributed in many sea areas around the world and also an aquacultured mollusc with high nutritional value.In this study,the whole soft body and the mantle tissue of black-shelled Pacifi c oyster(BSO)and white-shelled Pacifi c oyster(WSO)with starkly diff erent melanin contents were compared,and the diff erences in physiology and metabolism between BSO and WSO were analyzed.The results of physiological indicators suggested BSO show more melanin,more dry matter,more crude lipid content,and stronger ability to scavenge free radicals than WSO.The altered metabolites of glycerophospholipids,fatty acyls,and steroids revealed diff erent regulatory mechanisms of lipids.The correlation analysis of metabolomics and previously published RNAseq data suggested that BSO and WSO mainly diff ered in the basal metabolic processes,such as lipid,amino acid and purine metabolisms.This study provides insights into the changes in the physiological indictors and the metabolites of oysters with varying melanin content. | Xi CHEN Qiuyun JIANG Hongce SONG Lingling LI Chaoyi XIE Baoyu HUANG Yaqiong LIU Meiwei ZHANG Lei WEI Xiaotong WANG | 2021 | Journal of Oceanology and Limnology2021，39，1： | 2 |
| 4 | Wheat-RegNet:An encyclopedia of common wheat hierarchical regulatory networks显示文摘Dear Editor,Common wheat(Triticum aestivum,2n=6×=42,AABBDD)is the staple crop worldwide.Elucidating the gene regulatory network provides essential information for mechanism studies and targeted manipulation of gene activity for breeding.However,it is a challenging task given the extremely large(16 Gb)and complicated allohexaploid genome of common wheat.Integrating multi-omics data is a compelling approach to construct the hierarchical regulatory network. | Tengfei Tang Shilong Tian Haoyu Wang Xiaotong Lv Yilin Xie Jinyi Liu Meiyue Wang Fei Zhao Wenli Zhang Hao Li Yijing Zhang | 2023 | Molecular Plant2023，16，2： | 1 |
| 5 | A geological assessment method of floor water inrush risk and its application显示文摘 | Zhaoping Meng Guoqing Li Xiaotong Xie | 2012 | Engineering Geology2012，，： | 1 |
| 6 | Overexpression of Cdx2 inhibits progression of gastric cancer in vitro显示文摘 | Yubo Xie Lei Li Xiaotong Wang Yi Qin Qian Qian Xizi Yuan Qiang Xiao | 2010 | International Journal of Oncology2010，，2： | 1 |
| 7 | Enantioselective carboxylative cyclization of propargylic alcohol with carbon dioxide under mild conditions显示文摘An enantioselective carboxylative cyclization of propargylic alcohols and CO2 was realized under mild conditions,based on a kinetic resolution strategy,which enabled the synthesis of chiral cyclic carbonates and propargylic alcohols with promising yield and enantioselectivity simultaneously. | Shiliang Xie Xiaotong Gao Feng Zhou Haihong Wu Jian Zhou | 2020 | Chinese Chemical Letters2020，31，2： | 1 |
| 8 | Penalized Model--based Clustering with Cluster--specific Diagonal Covariance Matrices and Grouped Variables显示文摘 | Xie Benhuai Pan Wei Shen Xiaotong | 2008 | Electronic Journal of Statistics2008，，2： | 1 |
| 9 | DeepNitro: Prediction of Protein Nitration and Nitrosylation Sites by Deep Learning显示文摘Protein nitration and nitrosylation are essential post-translational modifications(PTMs)involved in many fundamental cellular processes. Recent studies have revealed that excessive levels of nitration and nitrosylation in some critical proteins are linked to numerous chronic diseases.Therefore, the identification of substrates that undergo such modifications in a site-specific manner is an important research topic in the community and will provide candidates for targeted therapy. In this study, we aimed to develop a computational tool for predicting nitration and nitrosylation sites in proteins. We first constructed four types of encoding features, including positional amino acid distributions, sequence contextual dependencies, physicochemical properties, and position-specificscoring features, to represent the modified residues. Based on these encoding features, we established a predictor called DeepNitro using deep learning methods for predicting protein nitration and nitrosylation. Using n-fold cross-validation, our evaluation shows great AUC values for DeepNitro, 0.65 for tyrosine nitration, 0.80 for tryptophan nitration, and 0.70 for cysteine nitrosylation, respectively,demonstrating the robustness and reliability of our tool. Also, when tested in the independent dataset, DeepNitro is substantially superior to other similar tools with a 7%à42% improvement in the prediction performance. Taken together, the application of deep learning method and novel encoding schemes, especially the position-specific scoring feature, greatly improves the accuracy of nitration and nitrosylation site prediction and may facilitate the prediction of other PTM sites. DeepNitro is implemented in JAVA and PHP and is freely available for academic research at http://gffzz99614c6466484d9dhwv0pn5qcowkk6uub.ffgz.tsg.suse.edu.cn. | Yubin Xie Xiaotong Luo Yupeng Li Li Chen Wenbin Ma Junjiu Huang Jun Cui Yong Zhao Yu Xue Zhixiang Zuo Jian Ren | 2018 | Genomics, Proteomics & Bioinformatics2018，16，4： | 1 |
| 10 | Relationship between heart rate and failure of biological valve: slowing the heart rate could delay the failure of biological valve?显示文摘For the patients with a relatively slow heart rate,the frequency of opening and closing of biological valves and the number of impact of mechanical stress upon biological valves were relatively less,so the mechanical wear was reduced.The question is whether this can slow the failure and calcification of the biological valve.A retrospective analysis of 92 biological mitral valve replacement (MVR) cases during the period of 1996-2003 was carried out. | Shi Qiuxia Hu Chuanxian Hou Xiaotong Jia Ming Xu Zhiwei Xie Jinsheng | 2014 | Chinese Medical Journal2014，，8： | 0 |
| 11 | Toward a stellar population catalog in the Kilo Degree Survey:The impact of stellar recipes on stellar masses and star formation rates显示文摘The Kilo Degree Survey(Ki DS)is currently the only sky survey providing optical(ugri)plus near-infrared(NIR,ZY H JKS)seeing matched photometry over an area larger than 1000 deg2.This is obtained by incorporating the NIR data from the VISTA Kilo Degree Infrared Galaxy(VIKING)survey,covering the same Ki DS footprint.As such,the Ki DS multi-wavelength photometry represents a unique dataset to test the ability of stellar population models to return robust photometric stellar mass(M_(*))and star-formation rate(SFR)estimates.Here we use a spectroscopic sample of galaxies for which we possess ugri ZY JHK_(s)“gaussianized”magnitudes from Ki DS data release 4.We fit the spectral energy distribution from the 9-band photometry using:(1)three different popular libraries of stellar population templates,(2)single burst,simple and delayed exponential star-formation history models,and(3)a wide range of priors on age and metallicity.As template fitting codes we use two popular softwares:Le Phare and CIGALE.We investigate the variance of the stellar masses and the star-formation rates from the different combinations of templates,star formation recipes and codes to assess the stability of these estimates and define some“robust”median quantities to be included in the upcoming Ki DS data releases.As a science validation test,we derive the mass function,the star formation rate function,and the SFR-M_(*)relation for a low-redshift(z<0.5)sample of galaxies,that result in excellent agreement with previous literature data.The final catalog,containing~290000 galaxies with redshift 0.01 | Linghua Xie Nicola R.Napolitano Xiaotong Guo Crescenzo Tortora Haicheng Feng Antonios Katsianis Rui Li Sirui Wu Mario Radovich Leslie K.Hunt Yang Wang Lin Tang Baitian Tang Zhiqi Huang | 2023 | Science China(Physics,Mechanics & Astronomy)2023，66，12： | 0 |
| 12 | Author correction to “A nanocleaner specifically penetrates the blood‒brain barrier at lesions to clean toxic proteins and regulate inflammation in Alzheimer’s disease” [Acta Pharmaceutica Sinica B 12, (2021) 4032e4044]显示文摘The authors regret that there were some picture errors in Fig.4A and data errors Fig.7A owing to the mistakes of copying and pasting in the process of assembling figures and making a dia-gram.The raw data of correct images of group b in Fig.4A and values of high dose in Fig.7A are provided in the supporting information,and the authors revise Figs.4 and 7 as below.The revisions do not affect any results and conclusions of the current work.The authors apologize for any inconvenience caused to the journal and readers. | Ting Lei Zhihang Yang Xue Xia Yuxiu Chen Xiaotong Yang Rou Xie Fan Tong Xiaolin Wang Huile Gao | 2022 | Acta Pharmaceutica Sinica B2022，12，6： | 0 |
| 13 | ULK1/2所构成的信号节点除控制细胞自噬外还控制葡萄糖代谢通路显示文摘在细胞感受到环境中营养物质和生长因子的提供量发生改变后,代谢通路的重编程对于维持此时胞内的稳态是非常重要的过程。ULK1和ULK2是传递外界应激信号至自噬发生的重要整合因子。 | Terytty Yang Li Yu Sun Yu Liang Qing Liu Yuzhe Shi Chen-Song Zhang Cixiong Zhang Lintao Song Pu Zhang Xianzhong Zhang Xiaotong Li Tao Chen Hui-Ying Huang Xiadi He Yi Wang Yu-Qing Wu Shaoxuan Chen Ming Jiang Canhe Chen Changchuan Xie James Y.Yang Yan Lin Shimin Zhao Zhiyun Ye Shu-Yong Lin Daniel Tsun-yee Chiu 林圣彩 | 2017 | 科学新闻2017，19，4： | 0 |
| 14 | VirusMap:A visualization database for the influenza A virus显示文摘Influenza A virus,a highly virulent pathogen that has caused several pandemic events over the course of human history,still remains a major threat to human health at present.The most serious influenza pandemic in recorded history was the 1918 Spanish flu outbreak,which killed about 20-100 million people worldwide(Murray et al.,2006).Also,the H5N1 virus was known for its | Yubin Xie Xiaotong Luo Zhihao He Yueyuan Zheng Zhixiang Zuo Qi Zhao Yanyan Miao Jian Ren | 2017 | Journal of Genetics and Genomics2017，44，5： | 0 |
| 15 | 阳离子通道TRPV在醛缩酶和AMPK感知葡萄糖过程中起必须的作用显示文摘文章简介在激活AMPK的溶酶体途径感应葡萄糖供给下降的过程中,果糖-1,6-二磷酸醛缩酶(aldolase)起关键作用。然而,醛缩酶是如何把其与果糖-1,6-二磷酸结合的减少的信息传导引起AMPK活化的机制还尚未清楚。 | Mengqi Li Chen-Song Zhang Yue Zong Jin-Wei Feng Teng Ma Meiqin Hu Zhizhong Lin Xiaotong Li Changchuan Xie Yaying Wu Dong Jiang Ying Li Cixiong Zhang Xiao Tian Wen Wang Yanyan Yang Jie Chen Jiwen Cui Yu-Qing Wu Xin Chen Qing-Feng Liu Jianfeng Wu Shu-Yong Lin Zhiyun Ye Ying Liu Hai-Long Piao Li Yu Zhuan Zhou Xiao-Song Xie D.Grahame Hardie 林圣彩 | 2020 | 科学新闻2020，，2： | 0 |
| 16 | Melatonin biosynthesis pathways in nature and its production in engineered microorganisms显示文摘Melatonin is a biogenic amine that can be found in plants,animals and microorganism.The metabolic pathway of melatonin is different in various organisms,and biosynthetic endogenous melatonin acts as a molecular signal and antioxidant protection against external stress.Microbial synthesis pathways of melatonin are similar to those of animals but different from those of plants.At present,the method of using microorganism fermentation to produce melatonin is gradually prevailing,and exploring the biosynthetic pathway of melatonin to modify microorganism is becoming the mainstream,which has more advantages than traditional chemical synthesis.Here,we review recent advances in the synthesis,optimization of melatonin pathway.L-tryptophan is one of the two crucial precursors for the synthesis of melatonin,which can be produced through a four-step reaction.Enzymes involved in melatonin synthesis have low specificity and catalytic efficiency.Site-directed mutation,directed evolution or promotion of cofactor synthesis can enhance enzyme activity and increase the metabolic flow to promote microbial melatonin production.On the whole,the status and bottleneck of melatonin biosynthesis can be improved to a higher level,providing an effective reference for future microbial modification. | Xiaotong Xie Dongqin Ding Danyang Bai Yaru Zhu Wei Sun Yumei Sun Dawei Zhang | 2022 | Synthetic and Systems Biotechnology2022，7，1： | 0 |
| 17 | Proton pitch angle distributions in the Martian induced magnetosphere: A survey of Tianwen-1 Mars Ion and Neutral Particle Analyzer observations显示文摘The pitch angle distributions of ions and electrons can be affected by various processes;thus,they can serve as an important indicator of the physical mechanisms driving the dynamics of space plasmas.From observations from the Mars Ion and Neutral Particle Analyzer onboard the Tianwen-1 orbiter,we calculated the pitch angle distributions of protons in the Martian induced magnetosphere by using information from the magnetohydrodynamically simulated magnetic field,and we statistically analyzed the spatial occurrence pattern of different types of pitch angle distributions.Even though no symmetrical features were seen in the dataset,we found the dominance of the field-aligned distribution type over the energy range from 188 to 6232 eV.Maps of the occurrence rate showed the preferential presence of a trapped-like distribution at the lower altitudes of the surveyed nightside region.Although our results are more or less restricted by the adopted magnetic field,they indicate the complexity of the near-Mars proton pitch angle distributions and infer the possibility of wave–particle interactions in the Martian induced magnetosphere. | TaiFeng Jin BinBin Ni LingGao Kong AiBing Zhang Lei Li Song Fu Xing Cao WenYa Li BinBin Tang LiangHai Xie YiTeng Zhang ShuYue Pang XiaoTong Yun HengLe Du FuHao Qiao LiMin Wang JiJie Ma | 2023 | Earth and Planetary Physics2023，7，5： | 0 |
| 18 | Identification of novel loci influencing refractive error in East Asian populations using an extreme phenotype design显示文摘The global 'myopia boom' has raised significant international concerns. Despite a higher myopia prevalence in Asia, previous large-scale genome-wide association studies(GWASs) were mostly based on European descendants. Here, we report a GWAS of spherical equivalent(SE) in 1852 Chinese Han individuals with extreme SE from Guangzhou(631 <-6.00 D and 574 > 0.00 D) and Wenzhou(593 <-6.00 D and54 >-1.75 D), followed by a replication study in two independent cohorts with totaling 3538 East Asian individuals. The discovery GWAS and meta-analysis identify three novel loci, which show genome-wide significant associations with SE, including 1 q25.2 FAM163 A, 10 p11.22 NRP1/PRAD3, and 10 p11.21 ANKRD30 A/MTRNR2 L7, together explaining 3.34% of SE variance. 10 p11.21 is successfully replicated.The allele frequencies of all three loci show significant differences between major continental groups(P < 0.001). The SE reducing(more myopic) allele of rs10913877(1 q25.2 FAM163 A) demonstrates the highest frequency in East Asians and much lower frequencies in Europeans and Africans(EAS = 0.60,EUR = 0.20, and AFR = 0.18). The gene-based analysis additionally identifies three novel genes associated with SE, including EI24, LHX5, and ARPP19. These results provide new insights into myopia pathogenesis and indicate the role of genetic heterogeneity in myopia epidemiology among different ethnicities. | Xiaotong Han Tianzi Liu Xiaohu Ding Jialin Liu Xingyan Lin Decai Wang Moeen Riaz Paul N.Baird Zhi Xie Yuan Cheng Yi Li Yuki Mori Masahiro Miyake Hengtong Li Ching-Yu Cheng Changqing Zeng Kyoko Ohno-Matsui Xiangtian Zhou Fan Liu Mingguang He | 2022 | Journal of Genetics and Genomics2022，49，1： | 0 |
| 19 | Significant discrepancies of land surface daily net radiation among ten remotely sensed and reanalysis products显示文摘Land surface all-wave net radiation(R_(n))is crucial in determining Earth’s climate by contributing to the surface radiation budget.This study evaluated seven satellite and three reanalysis long-term land surface R_(n)products under different spatial scales,spatial and temporal variations,and different conditions.The results showed that during 2000-2018,Global Land Surface Satellite Product(GLASS)-Moderate Resolution Imaging Spectroradiometer(MODIS)performed the best(RMSE=25.54 Wm^(-2),bias=-1.26 Wm^(-2)),followed by ERA5(the fifth-generation of European Centre for Medium-Range Weather Forecast Reanalysis)(RMSE=32.17 Wm^(-2),bias=-4.88 Wm^(-2))and GLASS-AVHRR(Advanced Very-High-Resolution Radiometer)(RMSE=33.10 Wm^(-2),bias=4.03 Wm^(-2)).During 1983-2018,GLASS-AVHRR and ERA5 ranked top and performed similarly,with RMSE values of 31.70 and 33.08 Wm^(-2)and biases of-4.56 and 3.48 Wm^(-2),respectively.The averaged multi-annual mean R_(n)over the global land surface of satellite products was higher than that of reanalysis products by about 10~30 Wm^(-2).These products differed remarkably in long-term trends variations,particularly pre-2000,but no significant trends were observed.Discrepancies were more frequent in satellite data,while reanalysis products showed smoother variations.Large discrepancies were found in regions with high latitudes,reflectance,and elevation which could be attributed to input radiative components,meteorological variables(e.g.,cloud properties,aerosol optical thickness),and applicability of the algorithms used.While further research is needed for detailed insights. | Xiuwan Yin Bo Jiang Shunlin Liang Shaopeng Li Xiang Zhao Qian Wang Jianglei Xu Jiakun Han Hui Liang Xiaotong Zhang Qiang Liu Yunjun Yao Kun Jia Xianhong Xie | 2023 | International Journal of Digital Earth2023，16，1： | 0 |
| 20 | CAR-T cells for cancer immunotherapy显示文摘Adoptive immunotherapy expressing synthetic chimeric antigen receptors(CAR)on T cells through in vitro modifications represents a new and innovative strategy in cancer treatment.This new approach enables T cells to recognize and bind tumor antigens via a single-chain variable fragment recognition domain,circumventing the restriction of major histocompatibility complex.This review summarized the structure/design of CAR-T cells and the evolution process this technology went through,displaying the theoretical foundation for CAR-T therapy,the marketed products and the latest preclinical and clinical research progress.Finally,we provided perspectives on this technology’s development and potential future applications,especially for treating hematological malignant and solid tumors. | Yangyang Xie Xiaotong Li Jingyi Wu Huiling Zeng Hamza Boucetta Binru Wang Pei Yang Wei He | 2023 | Chinese Chemical Letters2023，34，9： | 0 |
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