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| 1 | Gene expression signatures for phlegm-dampness constitution of Chinese Medicine显示文摘Dear Editor,The term'individualized medicine'was first used in Biochemistry Individuality in 1956 by Williams(Williams et al.,1956).With the emergence of the post-genome era in the21st century,individualized precision medicine has attracted increasing attention.In traditional Chinese medicine(TCM),there is also concept of individualized medicine,which is known as the Chinese constitutional theory,proposed in the1970s(Wang,2012).According to this theory,the | Lingru Li Juan Feng Haiqiang Yao Lan Xie Yu Chen Lingling Yang Shujuan Hou Shipeng Zhao Ranran Sun Yanling Wu Tongtong Bai Yingshuai Li Ruoxi Yu Ji Wang Qi Wang | 2017 | Science China(Life Sciences)2017，60，1： | 13 |
| 2 | Expression profiling-based clustering of healthy subjects recapitulates classifications defined by clinical observation in Chinese medicine显示文摘Differences between healthy subjects and associated disease risks are of substantial interest in clinical medicine. Based on clinical presentations, Traditional Chinese Medicine(TCM) classifies healthy people into nine constitutions: Balanced, Qi, Yang or Yin deficiency, Phlegm-dampness, Damp-heat, Blood stasis,Qi stagnation, and Inherited special constitutions. In particular, Yang and Yin deficiency constitutions exhibit cold and heat aversion, respectively. However, the intrinsic molecular characteristics of unbalanced phenotypes remain unclear. To determine whether gene expression-based clustering can recapitulate TCM-based classification, peripheral blood mononuclear cells(PBMCs) were collected from Chinese Han individuals with Yang/Yin deficiency(n ? 12 each) and Balanced(n ? 8) constitutions, and global gene expression profiles were determined using the Affymetrix HG-U133 A Plus 2.0 array. Notably,we found that gene expression-based classifications reflected distinct TCM-based subtypes. Consistent with the clinical observation that subjects with Yang deficiency tend toward obesity, series-clustering analysis detected several key lipid metabolic genes(diacylglycerol acyltransferase(DGAT2), acyl-Co A synthetase(ACSL1), and ATP-binding cassette subfamily A member 1(ABCA1)) to be down-and upregulated in Yin and Yang deficiency constitutions, respectively. Our findings suggest that Yin/Yang deficiency and Balanced constitutions are unique entities in their m RNA expression profiles. Moreover,the distinct physical and clinical characteristics of each unbalanced constitution can be explained, in part,by specific gene expression signatures. | Ruoxi Yu Dan Liu Yin Yang Yuanyuan Han Lingru Li Luyu Zheng Ji wang Yan Zhang Yingshuai Li Qian-Fei Wang Qi wang | 2017 | Journal of Genetics and Genomics2017，44，4： | 9 |
| 3 | Transcriptional landscape of rice roots at the single-cell resolution显示文摘There are two main types of root systems in flowering plants,namely taproot systems of dicots and fibrous root systems found in monocots.Despite this fundamental split,our current knowledge of cellular and molecular mechanism driving root development is mainly based on studies of the dicot model Arabidopsis.However,the world major crops are monocots and little is known about the transcriptional programs underlying cell-type specification in this clade.Here,we report the transcriptomes of more than 20000 single cells derived from root tips of two agronomically important rice cultivars.Using combined computational and experimental analyses we were able to robustly identify most of the major cell types and define novel cell-type-specific marker genes for both cultivars.Importantly,we found divergent cell types associated with specific regulatory programs,including phytohormone biosynthesis,signaling,and response,which were well conserved between the two rice cultivars.In addition,we detected substantial differences between the cell-type transcript profiles of Arabidopsis and rice.These species-specific features emphasize the importance of analyzing tissues across diverse model species,including rice.Taken together,our study provides insight into the transcriptomic landscape of major cell types of rice root tip at single-cell resolution and opens new avenues to study cell-type specification,function,and evolution in plants. | Qing Liu Zhe Liang Dan Feng Sanjie Jiang Yifan Wang Zhuoying Du Ruoxi Li Guihua Hu Pingxian Zhang Yanfei Ma Jan ULohmann Xiaofeng Gu | 2021 | Molecular Plant2021，14，3： | 9 |
| 4 | Allele-defined genome reveals biallelic differentiation during cassava evolution显示文摘Dear Editor,Generation of heterozygous genomes by hybridization between or within species can help maintain plant diversity and serve as a potential source of new species(Baek et al.,2018).Moreover,genomic heterozygosity is associated with genomic coadaptation,developmental stability,and heterosis.Accurate definition of alleles in haplotypes is necessary to precisely characterize allelic variation controlling agriculturally important traits(Shi et al.,2019).Currently,most released genomes have mosaic assembly of haplotypes due to random selection or collapse of alleles during genome assembly(Shi et al.,2019),which masked allelic variation and functional differentiation of divergent alleles in heterozygous species. | Wei Hu Changmian Ji Haitao shi Zhe Liang Zehong Ding Jianqiu Ye Wenjun Ou Gang Zhou Weiwei Tie Yan Yan Jinghao Yang Xiaoying Yang Yunxie Wei Zhiqiang Jin Jianghui Xie Ming Peng Wenquan Wang Anping Guo Biyu Xu Jianchun Guo Songbi Chen Liming Ma Mingcheng Wang Yang Zhou Xiaolong Li Ruoxi Li Siyi Guo Xinhui Xiao Zhongqing Wan Feifei An Jie Zhang Qingyun Leng Yin Li Ray Ming Kaimian Li | 2021 | Molecular Plant2021，14，6： | 8 |
| 5 | Rapid breeding of pink-fruited tomato hybrids using the CRISPR/Cas9 system显示文摘As one of the most important vegetables,tomato (Solanum lycopersicum) is extensively produced and consumed worldwide and substantially contributes to human nutrition and health (The Tomato Genome Consortium,2012).Although red tomatoes are the most common,pink tomatoes are more popular in Asia,particularly in China and Japan,because of their better taste (Ballester et al.,2010;Zhu et al.,2018).Compared with red tomatoes,pink tomatoes fail to accumulate the yellow-colored flavonoid pigment,naringenin chalcone (NarCh),in their peels,resulting in a colorless peel phenotype (Adato et al,2009;Ballester et al.,2010). | Tianxia Yang Lei Deng Wei Zhao Ruoxi Zhang Hongling Jiang Zhibiao Ye Chang-Bao Li Chuanyou Li | 2019 | Journal of Genetics and Genomics2019，46，10： | 8 |
| 6 | Dynamic modulation of innate immunity programming and memory显示文摘Recent progress harkens back to the old theme of immune memory, except this time in the area of innate immunity, to which traditional paradigm only prescribes a rudimentary first-line defense function with no memory. However, both in vitro and in vivo studies reveal that innate leukocytes may adopt distinct activation states such as priming, tolerance, and exhaustion, depending upon the history of prior challenges. The dynamic programming and potential memory of innate leukocytes may have far-reaching consequences in health and disease. This review aims to provide some salient features of innate programing and memory, patho-physiological consequences, underlying mechanisms, and current pressing issues. | Ruoxi Yuan Liwu Li | 2016 | Science China(Life Sciences)2016，59，1： | 4 |
| 7 | A Positive Correlation between Elevated Altitude and Frequency of Mutant Alleles at the EPAS1 and HBB Loci in Chinese Indigenous Dogs显示文摘Hypoxia represents one of the most extreme environmental conditions for both human beings and animals living at high altitudes(Zhao et al.,2009).Over the past few years,great attention has been focused on the genetic bases of adaption to high-altitude environments(Bigham et al.,2010;Simonson et al.,2010).The domestic dog(Canis familiaris)is the first animal that | Ruoxi Fan Fei Liu Hong Wu Shifang Wu Chunling Zhu Yan Li Guodong Wang Yaping Zhang | 2015 | Journal of Genetics and Genomics2015，42，4： | 4 |
| 8 | A hybrid genipin-crosslinked dual-sensitive hydrogel/nanostructured lipid carrier ocular drug delivery platform显示文摘The objective of this study was to develop a novel hybrid genipin-crosslinked dual-sensitive hydrogel/nanostructured lipid carrier(NLC) drug delivery platform. An ophthalmic antiinflammatory drug, baicalin(BN) was chosen as the model drug. BN –NLC was prepared using melt-emulsification combined with ultra-sonication technique. Additionally, a dual pH-and thermo-sensitive hydrogel composed of carboxymethyl chitosan(CMCS) and poloxamer 407(F127) was fabricated by a cross-linking reaction with a nontoxic crosslinker genipin(GP). GP-CMCS/F127 hydrogel was characterized by FTIR, NMR, XRD and SEM. The swelling studies showed GP-CMCS/F127 hydrogel was both pH-and thermo-sensitive. The results of in vitro release suggested BN –NLC gel can prolong the release of baicalin comparing with BN eye drops and BN –NLC. Ex vivo cornea permeation study was evaluated using Franz diffusion cells. The apparent permeability coefficient(Papp) of BN –NLC gel was much higher(4.46-fold) than that of BN eye drops. Through the determination of corneal hydration levels, BN –NLC gel was confirmed that had no significant irritation to cornea. Ex vivo precorneal retention experiments were carried out by a flow-through approach. The results indicated that the NLC-based hydrogel can prolong precorneal residence time. In conclusion, the hybrid NLCbased hydrogel has a promising potential for application in ocular drug delivery. | Yibin Yu Ruoxi Feng Jinyu Li Yuanyuan Wang Yiming Song Guoxin Tan Dandan Liu Wei Liu Xinggang Yang Hao Pan Sanming Li | 2019 | Asian Journal of Pharmaceutical Sciences2019，14，4： | 3 |
| 9 | Retro-enantio isomer of angiopep-2 assists nanoprobes across the blood-brain barrier for targeted magnetic resonance/fluorescence imaging of glioblastoma显示文摘Glioblastoma(GBM),one of the most common primary intracranial malignant tumours,is very difficult to be completely excised by surgery due to its irregular shape.Here,we use an MRI/NIR fluorescence dual-modal imaging nanoprobe that includes superparamagnetic iron oxide nanoparticles(SPIONs)modified with indocyanine(Cy7)molecules and peptides(ANG orDANG)to locate malignant gliomas and guide accurate excision.Both peptides/Cy7-SPIONs probes displayed excellent tumour-homing properties and barrier penetrating abilities in vitro. | Ruoxi Xie Zijun Wu Fanxin Zeng Huawei Cai Dan Wang Lei Gu Hongyan Zhu Su Lui Gang Guo Bin Song Jinxing Li Min Wu Qiyong Gong | 2021 | Signal Transduction and Targeted Therapy2021，6，9： | 3 |
| 10 | Safety,tolerability,and pharmacokinetics of BAT8001 in patients with HER2-positive breast cancer:An open-label,dose-escalation,phase I study显示文摘Background:The introductions of anti-human epidermal growth factor receptor-2(HER2)agents have significantly improved the treatment outcome of patients with HER2-positive breast cancer.BAT8001 is a novel antibodydrug conjugate targeting human epidermal growth factor receptor-2(HER2)-expressing cells composed of a trastuzumab biosimilar linked to the drug-linker Batansine.This dose-escalation,phase I study was designed to assess the safety,tolerability,pharmacokinetics,and preliminary anti-tumor activity of BAT8001 in patients with HER2-positive locally advanced or metastatic breast cancer.Methods:This trial was conducted in subjects with histologically confirmed HER2-positive breast cancer(having evaluable lesions and an Eastern Cooperative Oncology Group performance status of 0 or 1)using a 3+3 design of escalating BAT8001 doses.Patients received BAT8001 intravenously in a 21-day cycle,with dose escalation in 5 cohorts:1.2,2.4,3.6,4.8,and 6.0 mg/kg.The primary objective was to evaluate the safety and tolerability of BAT8001.Preliminary activity of BAT8001 was also assessed as a secondary objective.Results:Between March 2017 to May 2018,29 HER2-positive breast cancer patients were enrolled.The observed dose-limiting toxicities were grade 4 thrombocytopenia and grade 3 elevated transaminase.The maximum tolerated dose was determined to be 3.6 mg/kg.Grade 3 or greater adverse events(AEs)occurred in 14(48.3%)of 29 patients,including thrombocytopenia in 12(41.4%)patients,aspartate aminotransferase increased in 4(13.8%)patients,γ-glutamyl transferase increased in 2(6.9%)patients,alanine aminotransferase increased in 2(6.9%)patients,diarrhea in 2(6.9%)patients.Objective response was observed in 12(41.4%,95%confidence interval[CI]=23.5%-61.1%)and disease control(including patients achieving objective response and stable disease)was observed in 24(82.8%,95%CI=64.2%-94.2%)patients.Conclusions:BAT8001 demonstrated favorable safety profiles,with promising anti-tumor activity in patients with HER2-positive locally advanced or metastatic breast cancer.BAT8001 has the potential to provide a new therapeutic option in patients with metastatic HER2-positive breast cancer. | Ruoxi Hong Wen Xia Liye Wang Kaping Lee Qianyi Lu Kuikui Jiang Shengfeng Li Jinquan Yu Jin Wei Weijia Tang Danyang Zhou Xin An Jiajia Huang Cong Xue Xiwen Bi Yanxia Shi Zhongyu Yuan Fei Xu Shusen Wang | 2021 | Cancer Communications2021，41，2： | 2 |
| 11 | Consistency between traditional Chinese medicine constitution-based classification and genetic classification显示文摘Background:We studied the consistency between two classification systems for categorizing patients:traditional Chinese medicine(TCM)constitution-based methods,versus genetic clustering.Genetic classification in constitutional identification was also evaluated.Methods:A TCM physician evaluated the constitution of each patient,according to four examinations(inspection,auscultation-olfaction,interrogation,and palpation).Those who met the criteria for Yang-deficient,Yin-deficient,and balanced constitutions were enrolled in the study.Peripheral blood samples were obtained from the participants,and peripheral blood mononuclear cells were separated from the samples within 2 hours.Total RNA extraction from the white blood cells was performed;and an Affymetrix HG-U133 Plus2.0 array was used to determine the peripheral blood gene expression profiles.The samples were classified using a support vector machine genetic classifier,and the“leave-one-out”method was used for validation.Results:The global gene expression profiles of 32 samples were grouped into three categories,and the samples in each of the gene categories corresponded with the three constitution categories.The three constitution types were distinguished using the genetic classifier with 165 genes.The accuracy of the prediction classification was greater than 95%using mathematical method.Conclusions:Participants with Yin-deficient,Yang-deficient,and balanced constitutions have varying physical characteristics and gene expression patterns.Additionally,the results from TCM constitution classification matched those obtained by genetic classification.Finally,our preliminary gene classifier distinguishes among Yin-deficient,Yang-deficient,and balanced constitutions,and provides a methodological basis for identifying the different constitutions. | Ruoxi Yu Xiaohong Zhao Lingru Li Cheng Ni Yin Yang Yuanyuan Han Ji Wang Yan Zhang Qi Wang | 2015 | Journal of Traditional Chinese Medical Sciences2015，2，4： | 2 |
| 12 | Estimation of the age of human semen stains by attenuated total reflection Fourier transform infrared spectroscopy:a preliminary study显示文摘Semen stain is one of the most important biological evidence at sexual crime scenes.Age estimation of human semen stains plays an important role in forensic work,and it is rarely studied due to lack of well-established methods.In this study,the technique called attenuated total reflection Fourier transform infrared spectroscopy(ATR-FTIR)coupled with advanced chemometric methods was employed to determine the age of semen stains on three different substrates:glass slides,tissues and fabric made of regenerated cellulose fibres up to 6 d.Partial least squares regression(PLSR)was used in conjunction with spectral analysis for age estimation,and the results generated high R2 values(cross-validation:0.81,external validation:0.74)but a narrow margin of error for root mean square error(RMSE)(RMSE of cross-validation:0.77 d,RMSE of prediction:1.02 d).Additionally,our results indicated the robustness of PLSR model was not weaken by the influence of different substrates in this study.Our results indicate that ATR-FTIR,combined with chemometric methods,shows great potential as a convenient and efficient tool for age estimation of semen stains.Moreover,the method could be applied to routine forensic investigations in the future. | Shuai Zha Xin Wei Ruoxi Fang Qi Wang Hancheng Lin Kai Zhang Haohui Zhang Ruina Liu Zhouru Li Ping Huang Zhenyuan Wang | 2020 | Forensic Sciences Research2020，5，2： | 2 |
| 13 | The genomes of medicinal skullcaps reveal the polyphyletic origins of clerodane diterpene biosynthesis in the family Lamiaceae显示文摘The presence of anticancer clerodane diterpenoids is a chemotaxonomic marker for the traditional Chinese medicinal plant Scutellaria barbata,although the molecular mechanisms behind clerodane biosynthesis are unknown.Here,we report a high-quality assembly of the 414.98 Mb genome of S.barbata into 13 pseudochromosomes.Using phylogenomic and biochemical data,we mapped the plastidial metabolism of kaurene(gibberellins),abietane,and clerodane diterpenes in three species of the family Lamiaceae(Scutellaria barbata,Scutellaria baicalensis,and Salvia splendens),facilitating the identification of genes involved in the biosynthesis of the clerodanes,kolavenol,and isokolavenol.We show that clerodane biosynthesis evolved through recruitment and neofunctionalization of genes from gibberellin and abietane metabolism.Despite the assumed monophyletic origin of clerodane biosynthesis,which is widespread in species of the Lamiaceae,our data show distinct evolutionary lineages and suggest polyphyletic origins of clerodane biosynthesis in the family Lamiaceae.Our study not only provides significant insights into the evolution of clerodane biosynthetic pathways in the mint family,Lamiaceae,but also will facilitate the production of anticancer clerodanes through future metabolic engineering efforts. | Haixiu Li Song Wu Ruoxi Lin Yiren Xiao Ana Luisa Malaco Morotti Ya Wang Meytal Galilee Haowen Qin Tao Huang Yong Zhao Xun Zhou Jun Yang Qing Zhao Angelos K.Kanellis Cathie Martin Evangelos C.Tatsis | 2023 | Molecular Plant2023，16，3： | 2 |
| 14 | Thermospheric mass density derived from CHAMP satellite precise orbit determination data based on energy balance method显示文摘In this article, the energy balance method is used to retrieve thermospheric mass density from CHAMP satellite precise orbit determination(POD) data during 2007–2009. The retrieved thermospheric mass densities are compared with those from accelerometer data and an empirical model. The main conclusions are as follows:(1) Thermospheric mass density can be retrieved from POD data by the energy balance and semi-major axis decay methods, whose results are consistent.(2) The accuracy of the retrieved densities depends on the integration time period, and the optimal period for CHAMP density retrieval from POD data is about 20 minutes.(3) The energy balance method can be used to calibrate accelerometer data.(4) The accuracy of retrieving thermospheric density from POD data varies with satellite altitude and local time. | LI RuoXi LEI JiuHou WANG XiJing DOU XianKang JIN ShuangGen | 2017 | Science China Earth Sciences2017，60，8： | 2 |
| 15 | Conservation and ecofriendly utilization of wetlands assoeiated with the Three Gorges Reservoir 显示文摘 | WILLISON J H M LI Ruoxi YUAN Xingzhong | 2013 | Environmental Science and Pollution Research2013，20，10： | 1 |
| 16 | Defect of SLC38A3 promotes epithelial-mesenchymal transition and predicts poor prognosis in esophageal squamous cell carcinoma显示文摘Objective: Solute carrier family 38(SLC38 s) transporters play important roles in amino acid transportation and signaling transduction. However, their genetic alterations and biological roles in tumors are still largely unclear.This study aimed to elucidate the genetic signatures of SLC38 s transporters and their implications in esophageal squamous cell carcinoma(ESCC).Methods: Analyses on somatic mutation and copy number alterations(CNAs) of SLC38 A3 were performed as described. Immunohistochemistry(IHC) assay and Western blot assay were used to detect the protein expression level. MTS assay, colony formation assay, transwell assay and wound healing assay were used to explore the malignant phenotypes of ESCC cells. Immunofluorescence assay was used to verify the colocalization of two indicated proteins and immunopreciptation assay was performed to confirm the interaction of proteins.Results: Our findings revealed that SLC38 s family was significantly disrupted in ESCC, with high frequent CNAs and few somatic mutations. SLC38 A3 was the most frequent loss gene among them and was linked to poor survival and lymph node metastasis. The expression of SLC38 A3 was lower in tumor tissues compared to that in normal tissues, which was also significantly associated with worse clinical outcome. Further experiments revealed that depletion of SLC38 A3 could promote EMT in ESCC cell lines, and the interaction of SLC38 A3 and SETDB1 might lead to the reduced transcription of Snail. Pharmacogenomic analyses demonstrated that fifteen inhibitors were showed significantly correlated with SLC38 A3 expression.Conclusions: Our investigations have provided insights that SLC38 A3 could act as a suppressor in EMT pathway and serve as a prognostic factor and predictor of differential drug sensitivities in ESCC. | Rui Liu Ruoxi Hong Yan Wang Ying Gong Danna Yeerken Di Yang Jinting Li Jiawen Fan Jie Chen Weimin Zhang Qimin Zhan | 2020 | Chinese Journal of Cancer Research2020，32，5： | 1 |
| 17 | Microstructures and thermochromic characteristics of low-cost vanadium–tungsten co-sputtered thin films显示文摘 | Sheng Zhou Yi Li Huiqun Zhu Ruoxi Sun Yuming Zhang Yize Huang Liu Li Yujian Shen Qiuxin Zhen Guoxiang Tong Baoying Fang | 2011 | Surface & Coatings Technology (-)2011，，11： | 1 |
| 18 | Preeclampsia and gesta- tional diabetes mellitus uric acid changes and significance of serum 显示文摘 | Li Kehong Ruoxi Ouyang Bin | 2012 | Journal of Gannan School of Medicine2012，，3： | 1 |
| 19 | Multifunctional semitransparent organic solar cells with excellent infrared photon rejection显示文摘Semitransparent organic solar cells(ST-OSCs)have the potentials to open promising applications that differ from those of conventional inorganic ones,such as see-through power windows with both energy generation and heat insulation functions.However,to achieve so,there remain significant challenges,especially for balancing critical parameters,such as power conversion efficiency(PCE),average visible transparency(AVT)and low energy infrared photon radiation rejection(IRR)to realize the full potentials of ST-OSCs.Herein,we demonstrate the new design of ST-OSCs through the rational integration of organic materials,transparent electrode and infrared photon reflector in one device.With the assistance of optical simulation,new ST-OSCs with precise layout exhibit state-of-art performance,with near 30%AVT and PCE of 7.3%,as well as an excellent IRR of over 93%(780-2500 nm),representing one of best multifunctional ST-OSCs with promising perspective for window application. | Xue Li Ruoxi Xia Kangrong Yan Hin-Lap Yip Hongzheng Chen Chang-Zhi Li | 2020 | Chinese Chemical Letters2020，31，6： | 1 |
| 20 | Preeclampsia and gestational diabetes mellitus uric acid changes and significance of serum显示文摘 | Li Kehong Ruoxi Ouyang Bin | 2012 | Journal of Gannan School of Medicine2012，，3： | 1 |
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