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| 1 | Base-Editing-Mediated Artificial Evolution of OsALS1 In Planta to Develop Novel Herbicide-Tolerant Rice Germplasms显示文摘Recently developed CRISPR-mediated base editors,which enable the generation of num erous nucleotide changes in target genomic regions,have been widely adopted for gene correction and generation of crop germ plasms containing im portant gain-of-function genetic variations.How ever,to engineer target genes with unknown functional SNPs remains challenging.To address this issue,we present here abase-e diting-mediated gene evolution(BEMGE)m ethod,employing both Cas9n-based cytosine and adenine base editors as well as a single-guide RNA(sgRNA)library tiling the full-length coding region,for developing novel rice germ plasm swith mutations in any endogenous gene.To this end,OsALS1 was artificially evolved in rice cells using BEMGE through both Agrobacterium-mediated and particle-bom bardment-mediated transform ation.Four different types of amino acid substitutions in the evolved OsALS1,derived from two sites that have never been targeted by natural or human selection during rice dom estication,were identified,conferring varying levels of tolerance to the herbicide bispyribac-sodium.Furtherm ore,the P171F substitution identified in a strong OsALS1 allele was quickly introduced into the commercial rice cultivar Nangeng 46 through precise base editing w ith the corresponding base editor and sgRNA.Collectively,these data indicate great potential of BEMGE in creating important genetic variants of target genes for crop improvement. | Yongjie Kuang Shaofang Li Bin Ren Fang Yan Carl Spetz Xiangju Li Xueping Zhou Huanbin Zhou | 2020 | Molecular Plant2020，13，4： | 37 |
| 2 | AXL is a candidate receptor for SARS-CoV-2 that promotes infection of pulmonary and bronchial epithelial cells显示文摘The current coronavirus disease 2019(COVID-19)pandemic presents a global public health challenge.The viral pathogen responsible,severe acute respiratory syndrome coronavirus 2(SARS-CoV-2),binds to the host receptor ACE2 through its spike(S)glycoprotein,which mediates membrane fusion and viral entry.Although the role of ACE2 as a receptor for SARS-CoV-2 is clear,studies have shown that ACE2 expression is extremely low in various human tissues,especially in the respiratory tract.Thus,other host receptors and/or co-receptors that promote the entry of SARS-CoV-2 into cells of the respiratory system may exist.In this study,we found that the tyrosine-protein kinase receptor UFO(AXL)specifically interacts with the N-terminal domain of SARS-CoV-2 S.Using both a SARS-CoV-2 virus pseudotype and authentic SARS-CoV-2,we found that overexpression of AXL in HEK293T cells promotes SARS-CoV-2 entry as efficiently as overexpression of ACE2,while knocking out AXL significantly reduces SARS-CoV-2 infection in HI 299 pulmonary cells and in human primary lung epithelial cells.Soluble human recombinant AXL blocks SARS-CoV-2 infection in cells expressing high levels of AXL.The AXL expression level is well correlated with SARS-CoV-2 S level in bronchoalveolar lavage fluid cells from COVID-19 patients.Taken together,our findings suggest that AXL is a novel candidate receptor for SARS-CoV-2 which may play an important role in promoting viral infection of the human respiratory system and indicate that it is a potential target for future clinical intervention strategies. | Shuai Wang Zongyang Qiu Yingnan Hou Xiya Deng Wei Xu Tingting Zheng Peihan Wu Shaofang Xie Weixiang Bian Chong Zhang Zewei Sun Kunpeng Liu Chao Shan Aifu Lin Shibo Jiang Youhua Xie Qiang Zhou Lu Lu Jing Huang Xu Li | 2021 | Cell Research2021，31，2： | 39 |
| 3 | Cas9-NG Greatly Expands the Targeting Scope of the Genome-Editing Toolkit by Recognizing NG and Other Atypical PAMs in Rice显示文摘CRISPR technologies enabling precise genome manipulation are valuable for gene function studies and molecular crop breeding. However, the requirement of a protospacer adjacent motif (PAM)y such as NGG and TTN, for Cas protein recognition restricts the selection of targetable genomic loci in practical applications of CRISPR technologies. Recently Cas9-NG, which recognizes a minimal NG PAM, was reported to expand the targeting space of genome editing in human cells, but it remains unclear whether this Cas9 variant can be used in plants. In this study, we evaluated the nuclease activity of Cas9-NG toward various NGN PAMs by targeting endogenous genes in transgenic rice. We found that Cas9-NG edits all NGG, NGA, NGT, and NGC sites with impaired activity, while the gene-edited plants were dominated by monoallelic mutations. Cas9-NG-engineered base editors were then developed and used to generate O s B Z R I gainof- function plants that can not be created by other available Cas9-engineered base editors. Moreover, we showed that a Cas9-NG-based transcriptional activator efficiently upregulated the expression of endogenous target genes in rice. In addition, we discovered that Cas9-NG recognizes NAC, NTG, NTT, and NCG apart from NG PAM. Together, these findings demonstrate that Cas9-NG can greatly expand the targeting scope of genome-editing tools, showing great potential for targeted genome editing, base editing, and genome regulation in plants. | Bin Ren Lang Liu Shaofang Li Yongjie Kuang Jingwen Wang Dawei Zhang Xueping Zhou Honghui Lin Huanbin Zhou | 2019 | Molecular Plant2019，12，7： | 18 |
| 4 | On deep holes of standard Reed-Solomon codes显示文摘Determining deep holes is an important open problem in decoding Reed-Solomon codes. It is well known that the received word is trivially a deep hole if the degree of its Lagrange interpolation polynomial equals the dimension of the Reed-Solomon code. For the standard Reed-Solomon codes [p-1, k]p with p a prime, Cheng and Murray conjectured in 2007 that there is no other deep holes except the trivial ones. In this paper, we show that this conjecture is not true. In fact, we find a new class of deep holes for standard Reed-Solomon codes [q-1, k]q with q a power of the prime p. Let q≥4 and 2≤k≤q-2. We show that the received word u is a deep hole if its Lagrange interpolation polynomial is the sum of monomial of degree q-2 and a polynomial of degree at most k-1. So there are at least 2(q-1)qk deep holes if k q-3. | WU RongJun HONG ShaoFang | 2012 | Science China Mathematics2012，55，12： | 9 |
| 5 | High-efficiency and multiplex adenine base editing in plants using new TadA variants显示文摘Recently reported adenine base editors(ABEs)exhibit powerful potential for targeted gene correction as well as developing gain-of-function mutants and novel germplasms for both gene function studies and crop breeding.However,editing efficiency varies significantly among different target sites.Here,we investigated the activities of three evolved E.coli adenosine deaminase TadA variants(TadA8e,TadA8.17,and TadA8.20)side-by-side in transgenic rice.We found that TadA8e outperforms TadA8.17 and TadA8.20,and induces efficient A-to-G conversion at all tested sites in the rice genome,including those that were un-editable by ABE7.10 in our previous experiments.Furthermore,V82S/Q154R mutations were incorporated into TadA8e,resulting in a new variant that we named TadA9.Our data show that TadA9 is broadly compatible with CRISPR/SpCas9,CRISPR/SpCas9-NG,and CRISPR/SpRY,as well as CRISPR/ScCas9 nickase systems,achieving comparable or enhanced editing in a larger editing window at diverse PAM sites as compared with TadA8e.Finally,TadA9 was used to simultaneously install novel SNPs in four endogenous herbicide target genes in the commercial rice cultivar Nangeng 46 for potential field application in.weed control.Collectively,we successfully generated a series of novel ABEs that can efficiently edit adenosines in the rice genome.Our findings suggest that TadA9 and TadA8e have great potentials in the development of plant base editors and crop molecular breeding. | Daqi Yan Bin Ren Lang Liu Fang Yan Shaofang Li Guirong Wang Wenxian Sun Xueping Zhou Huanbin Zhou | 2021 | Molecular Plant2021，14，5： | 8 |
| 6 | Effect of Banxia Xiexin decoction on Helicobacter pylori-related peptic ulcers and its possible mechanism via the TGF-β/Smad signaling pathway显示文摘OBJECTIVE: To investigate the effect of Banxia Xiexin decoction(BXD) on Helicobacter pylori(Hp)-related peptic ulcers(PUs) and the possible mecha-nism underlying BXD actions via the transforming growth factor-β/small mothers against decapentaplegic(TGF-β/Smad) signaling pathway.METHODS: PU patients with cold-heat complex syndrome were randomly assigned to groups that received Chinese or Western medicines with 20 patients in each group. Serum was collected after 7 d of treatment. The healthy group included 20 individuals. Gastric mucosal epithelial cell line GES-1 was cultured in vitro and randomly divided into the following seven groups: control, model, healthy,Western Medicine, prior treatment, low dosage,and high dosage. After 72 h of treatment with the corresponding serum, the m RNA and protein expression levels of TGF-β1, Smad3, and Smad7 were measured by reverse transcription quantitative polymerase chain reaction and western blotting, respectively.RESULTS: The m RNA expression levels of TGF-β1 and Smad3 in GES-1 cells were increased after Hp introduction, and these increased levels were reduced by the BXD-containing serum. The protein levels of p-Smad3, but not TGF-β1 or Smad3, were significantly increased in Hp-treated GES-1 cells,and treatment with the BXD-containing serum markedly decreased the protein levels. Smad7 expression was significantly enhanced following treatment with the BXD-containing serum at transcriptional and protein levels in a dose-dependent manner.CONCLUSION: BXD regulates the TGF-β/Smad signaling pathway by inhibiting the expression of TGF-β1 and Smad3, and increasing the expression of Smad7. | Chen Shaofang Liang Huiqing Chen Shaodong Huang Yanping Wan Shichuan Huang Yanxia | 2018 | Journal of Traditional Chinese Medicine2018，38，3： | 7 |
| 7 | Effect of a comprehensive therapy plus Gushenyutai plaster administered at Guanyuan(CV 4) on male infertility associated with semen non-liquefaction显示文摘OBJECTIVE: To observe the clinical effect of Gushenyutai plaster administered at the Guanyuan(CV4) acupoint on male infertility associated with semen non-liquefaction.METHODS: Sixty-two male patients with infertility caused by semen non-liquefaction were random-ized into a treatment and control group. The control group received comprehensive therapy, which included oral administration of clarithromycin sustained release tablets, hip bath with Zhongyaoxiaoyan granules, prostate massage, and transurethral microwave treatment. The treatment group was administered Gushenyutai plaster in addition to the comprehensive therapy. Both groups were treated for 8 weeks. After treatment, the clinical effect and pregnancy rate were assessed and compared between the two groups.RESULTS: The effective rate of the treatment group was significantly higher than that of the control group(96.77% vs 70.97%, P<0.05) and the pregnancy rates of the treatment group and control groups were 38.71% and 16.13%, respectively(P<0.05).CONCLUSION: The effect of Gushenyutai plaster plus comprehensive therapy was better than that of the comprehensive therapy alone on male infertility induced by semen non-liquefaction. | Shaofang Peng Yanping Zheng Kangzhuang Zheng Ke Lin Juhong Wu Wenqin Zheng Yongzhong Li Yang Li Chuangjian Lin | 2014 | Journal of Traditional Chinese Medicine2014，34，6： | 6 |
| 8 | A Hybrid FCW-EMD and KF-BA-SVM Based Model for Short-term Load Forecasting显示文摘This paper proposes a hybrid short-term load forecasting method,which is based on the fuzzy combination weights as well as the empirical mode decomposition process(FCW-EMD),and support vector machine optimized via the Bat algorithm as well as the Kalman filtering process(KF-BA-SVM).The subjective weight is presented as a new theory and is applied to capture the inherent correlation effectively among hourly loads.Based on the proposed objective weights and subjective weights,the fuzzy combination weights theory(FCW)-a new similar day selection theory is presented,which improves the accuracy of the similar day selection,and correspondingly,makes the original data for EMD processing decrease dramatically.BA is introduced to optimize parameters of the SVM model for further improving the forecasting accuracy.Using the decomposed load series via empirical model decomposition(EMD)as inputs to SVM and further correcting the output of SVM via KF,a hybrid FCW-EMD and KF-BA-SVM short-term load forecasting method is established.Numerical case studies on the load forecasting of a transformer substation in south China show that the proposed hybrid forecasting model outperforms other forecasting methods and effectively improves the prediction accuracy. | Qingzhen Liu Yuanbin Shen Lei Wu Jie Li Lirong Zhuang Shaofang Wang | 2018 | CSEE Journal of Power and Energy Systems2018，4，2： | 6 |
| 9 | Highly efficient extraction of lithium from salt lake brine by LiAl-layered double hydroxides as lithium-ion-selective capturing material显示文摘The extraction of lithium from salt lake brine in the Chinese Qaidam Basin is challenging due to its high Mg/Li and Na/Li ratios. Herein, we utilized a reaction-coupled separation technology to separate sodium and lithium ions from a high Na/Li ratio brine(Na/Li = 48.7, w/w) and extracted lithium with Li Al-layered double hydroxides(Li Al-LDHs). The Li Al-LDHs act as lithium-ion-selective capturing materials from multication brines. That is, the lithium ions selectively enter the solid phase to form Li Al-LDHs, and the sodium ions are still retained in the liquid phase. This is because the lithium ions can be incorporated into the structural vacancies of LiAl-LDHs, whereas the sodium ions cannot. The effects of reaction conditions on lithium loss and separation efficiency were investigated at both the nucleation and the crystallization stage, e.g., the nucleation rotating speed, the Li/Al molar ratio, the crystallization temperature and time, and co-existing cations. The lithium loss is as low as 3.93% under optimal separation conditions.The sodium ions remained in the solution. Consequently, an excellent Na/Li separation efficiency was achieved by this reaction-coupled separation technology. These findings confirm that LiAl-LDHs play a critical function in selectively capturing lithium ions from brines with a high Na/Li ratio, which is useful for the extraction of lithium ions from the abundant salt lake brine resources in China. | Ying Sun Xiaoyu Guo Shaofang Hu Xu Xiang | 2019 | Journal of Energy Chemistry2019，28，7： | 5 |
| 10 | Fast-Suppressor Screening for New Components in Protein Trafficking,Organelle Biogenesis and Silencing Pathway in Arabidopsis thaliana Using DEX-Inducible FREE1-RNAi Plants显示文摘Membrane trafficking is essential for plant growth and responses to external signals.The plant unique FYVE domain-containing protein FREE1 is a component of the ESCRT complex(endosomal sorting complex required for transport).FREE1 plays multiple roles in regulating protein trafficking and organelle biogenesis including the formation of intraluminal vesicles of multivesicular body(MVB),vacuolar protein transport and vacuole biogenesis,and autophagic degradation.FREE1 knockout plants show defective MVB formation,abnormal vacuolar transport,fragmented vacuoles,accumulated autophagosomes,and seedling lethality.To further uncover the underlying mechanisms of FREE1 function in plants,we performed a forward genetic screen for mutants that suppressed the seedling lethal phenotype of FREE1-RNAi transgenic plants.The obtained mutants are termed as suppressors of free1(sof).To date,229 putative sof mutants have been identified.Barely detecting of FREE1 protein with M3plants further identified 84 FREE1-related suppressors.Also145 mutants showing no reduction of FREE1 protein were termed as RNAi-related mutants.Through next-generation sequencing(NGS)of bulked DNA from F2mapping population of two RNAi-related sof mutants,FREE1-RNAi T-DNA inserted on chromosome 1 was identified and the causal mutation of putative sof mutant is being identified similarly.These FREE1-and RNAi-related sof mutants will be useful tools and resources for illustrating the underlying mechanisms of FREE1 function in intracellular trafficking and organelle biogenesis,as well as for uncovering the new components involved in the regulation of silencing pathways in plants. | Qiong Zhao Caiji Gao PoShing Lee Lin Liu Shaofang Li Tangjin Hu Jinbo Shen Shuying Pan Hao Ye Yunru Chen Wenhan Cao Yong Cui Peng Zeng Sheng Yu Yangbin Gao Liang Chen Beixin Mo Xin Liu Shi Xiao Yunde Zhao Silin Zhong Xuemei Chen Liwen Jiang | 2015 | Journal of Genetics and Genomics2015，42，6： | 4 |
| 11 | Mutant p53 promotes cell spreading and migration via ARHGAP44显示文摘The tumor suppressor p53 protein is either lost or mutated in about half of all human cancers.Loss of p53 function is well known to influence cell spreading,migration and invasion.While expression of mutant p53 is not equivalent to p53 loss,mutant p53 can acquire new functions to drive cell spreading and migration via different mechanisms.In our study,we found that mutant p53 significantly increased cell spreading and migration when comparing with p53-null cells.RNA-Seq analysis suggested that Rho GTPase activating protein 44(ARHGAP44) is a new target of mutant p53,which suppressed AKHGAP44 transcription.ARHGAP44 has GAP activity and catalyze GTP hydrolysis on Cdc42.Higher level of GTP-Cdc42 was correlated with increase expression of mutant p53 and reduced ARHGAP44.Importantly,wt-ARHGAP44 but not mutant ARHGAP44(R291A) suppressed mutant p53 mediated cell spreading and migration.Bioinformatics analysis indicated lower expression of ARHGAP44 in lung carcinoma compared with normal tissues,which was verified by RT-qPCR using specimens from patients.More interestingly,ARHGAP44 mRNA level was lower in tumors with mutant p53 than those with normal p53.Collectively,our results disclose a new mechanism by which mutant p53 stimulates cell spreading and migration. | Jinjin Xu Jian Jiao Wei Xu Lei Ji Dongjie Jiang Shaofang Xie Syeda Kubra Xiaotao Li Junjiang Fu Jianru Xiao Bianhong Zhang | 2017 | Science China(Life Sciences)2017，60，9： | 4 |
| 12 | Additive characters and orthogonal systems of polynomials in several indeterminates over residue class rings显示文摘Let m, n and k be positive integers, m>1 and k≤n . Let Z m =Z/ m Z denote the residue class ring modulo m . Let Z denote the group of additive characters of ring Z m , x 0 denote the identity of Z . A necessary and sufficient condition for the system f\-1, ..., f\-k∈ Z m [ x\-1, ..., x\-n ] to be orthogonal is given: for all additive characters ψ 1, ..., ψ k ∈Z with ψ i≠x 0 for some i, 1≤i≤k, ∑(c\-1, ..., c\-n)∈ Z n m ψ(f\-1(c\-1, ..., c\-n))...ψ k(f\-k(c\-1, ..., c\-n))=0. As corollaries, the result of Shiue_Sun_Zhang and the result of Sun are obtained. | HONG Shaofang Department of Mathematics, Sichuan University, Chengdu 610064, China | 1998 | Chinese Science Bulletin1998，43，4： | 3 |
| 13 | Sequence analysis of the Microcystis aeruginosa FACHB-912 phytochrome gene supports positive selection in cyanobacteria显示文摘The phytochrome gene from Microcystis aeruginosa FACHB-912,isolated from algal blooms in Taihu Lake in China,was sequenced and found to code for a wavelength transition light receptor protein.The gene was composed of five distinct domains:a PAS fold domain,a GAF domain,a phytochrome domain,a His Kinase A(phosphoacceptor) domain,and a histidine kinase domain.Red-absorbing phytochrome,far-red-absorbing phytochrome,and photoconversion kinetics were monitored via the spectral characteristics of the protein.To detect positive selection,homologous sequences from cyanobacterium phytochrome genes were obtained from GenBank.Potential selective pressure was identified by phylogenetic analysis with maximum likelihood analyses.The frequency of the phytochrome gene being subjected to selective constraints suggests that positive selection is a potentially important mechanism that promotes the evolution of the cyanobacteria phytochrome gene.The sites identified in this study provide targets for further research on the structural-functional role of these residues,and on the correlation with the mechanism of algal blooms. | SHI Fei LI Nan LIU ShaoFang QIN Song | 2012 | Chinese Science Bulletin2012，57，25： | 2 |
| 14 | Multifunctional SnO2/3D graphene hybrid materials for sodium-ion and lithium-ion batteries with excellent rate capability and long cycle life显示文摘 | Jung-ln Lee Junhua Song Younghwan Cha Shaofang Fu Chengzhou Zhu Xiaolin Li Yuehe Lin Min-Kyu Song | 2017 | Nano Research2017，10，12： | 2 |
| 15 | Influence of proximity to the Qinghai-Tibet highway and railway on variations of soil heavy metal concentrations and bacterial community diversity on the Tibetan Plateau显示文摘An understanding of soil microbial communities is crucial in roadside soil environmental assessments.The 16S rRNA se quencing of a stressed microbial community in soil adjacent to the Qinghai-Tibet Highway(QTH)revealed that the accu mulation of heavy metals(over about 10 years)has affected the diversity of bacterial abundance and microbial community structure.The proximity of a sampling site to the QTH/Qinghai-Tibet Railway(QTR),which is effectively a measure of the density of human engineering,was the dominant factor influencing bacterial community diversity.The diversity of bacterial communities shows that 16S rRNA gene abundance decreased in relation to proximity to the QTH and QTR in both alpine wetland and meadow areas.The dominant phyla across all samples were Actinobacteria and Proteobacteria.The concentration of Cr and Cd in the soil were positively correlated with proximity to the QTH and QTR(MC/WC sam pling sites),and Ni,Co,and V were positively correlated with proximity to the QTH and QTR(MA/WA sampling sites).The results presented in this study provide an insight into the relationships among heavy metals and soil microbial commu nities,and have important implications for assessing and predicting the impacts of human-induced activities from the QTH and QTR in such an extreme and fragile environment. | Xia Zhao JunFeng Wang Yun Wang Xiang Lu ShaoFang Liu YuBao Zhang ZhiHong Guo ZhongKui Xie RuoYu Wang | 2019 | Research in Cold and Arid Regions2019，11，6： | 2 |
| 16 | SUMOylation-modified Pelota-Hbs1 RNA surveillance complex restricts the infection of potyvirids in plants显示文摘RNA quality control nonsense-mediated decay is involved in viral restriction in both plants and animals.However,it is not known whether two other RNA quality control pathways,nonstop decay and no-go decay,are capable of restricting viruses in plants.Here,we show that the evolutionarily conserved Pelota–Hbs1 complex negatively regulates infection of plant viruses in the family Potyviridae(termed potyvirids),the largest group of plant RNA viruses that accounts for more than half of the viral crop damage worldwide.Pelota enables the recognition of the functional G1-2A6-7 motif in the P3 cistron,which is conserved in almost all potyvirids.This allows Pelota to target the virus and act as a viral restriction factor.Furthermore,Pelota interacts with the SUMO E2-conjugating enzyme SCE1 and is SUMOylated in planta.Blocking Pelota SUMOylation disrupts the ability to recruit Hbs1 and inhibits viral RNA degradation.These findings reveal the functional importance of Pelota SUMOylation during the infection of potyvirids in plants. | Linhao Ge Buwei Cao Rui Qiao Hongguang Cui Shaofang Li Hongying Shan Pan Gong Mingzhen Zhang Hao Li Aiming Wang Xueping Zhou Fangfang Li | 2023 | Molecular Plant2023，16，3： | 2 |
| 17 | A novel magnetic biochar efficiently sorbs organic pollutants and phosphate显示文摘 | Chen Baoliang Chen Zaiming Lv Shaofang | 2011 | Bioresource Technology2011，102，： | 1 |
| 18 | Template-directed synthesis of nitrogen- and sulfur- codoped carbon nanowire aerogels with enhanced electrocatalytic performance for oxygen reduction显示文摘做的 Heteroatom,精确作文控制,和合理形态学设计是为在燃料房间为氧减小反应(ORR ) 生产新奇 nanocatalysts 的有效策略。此处,综合的一条划算的途径用一个难 templating 方法的 nitrogen-codoped 和 sulfur-codoped 碳 nanowire aerogels 被建议。aerogels 在碱的答案为 ORR 用热水的处理和碳化展览的联合准备了好催化活动。在在氮和硫先锋之间的最佳的退火温度和集体比率,结果的 aerogels 表演可比较的 electrocatalytic 活动到为 ORR 的商业 Pt/C 催化剂的。重要地,优化催化剂为甲醇转线路效果显示出更好长期的稳定性和令人满意的忍耐。这些 codoped aerogels 被期望在燃料房间有潜在的应用。 | Shaofang Fu Chengzhou Zhu Junhua Song Mark H. Engelhard Xiaolin Li Peina Zhang Haibing Xia Dan Du Yuehe Lin | 2017 | Nano Research2017，10，6： | 1 |
| 19 | A novel magnetic biochar efficiently sorbs organic pollutants and phosphate显示文摘 | Chen Baoliang Chen Zaiming Lv Shaofang | 2011 | Bioresource Tech- nology2011，102，： | 1 |
| 20 | Growth and spectral properties of Nd^3 + -doped Sr3Gd ( BO3 ) 3 crystal显示文摘 | Pan Jianguo Wu ShaoFang Wang Guofu | 2005 | Optical materials2005，，： | 1 |
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