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Hong‑Ying Wei,Sheng Huang,Jiang‑Yong Wang,Fang Gao,Jing‑Zhe Jiang 한국유전학회 2018 Genes & Genomics Vol.40 No.3
The emergence and widespread use of high-throughput sequencing technologies have promoted metagenomic studies on environmental or animal samples. Library construction for metagenome sequencing and annotation of the produced sequence reads are important steps in such studies and influence the quality of metagenomic data. In this study, we collected some marine mollusk samples, such as Crassostrea hongkongensis, Chlamys farreri, and Ruditapes philippinarum, from coastal areas in South China. These samples were divided into two batches to compare two library construction methods for shellfish viral metagenome. Our analysis showed that reverse-transcribing RNA into cDNA and then amplifying it simultaneously with DNA by whole genome amplification (WGA) yielded a larger amount of DNA compared to using only WGA or WTA (whole transcriptome amplification). Moreover, higher quality libraries were obtained by agarose gel extraction rather than with AMPure bead size selection. However, the latter can also provide good results if combined with the adjustment of the filter parameters. This, together with its simplicity, makes it a viable alternative. Finally, we compared three annotation tools (BLAST, DIAMOND, and Taxonomer) and two reference databases (NCBI’s NR and Uniprot’s Uniref). Considering the limitations of computing resources and data transfer speed, we propose the use of DIAMOND with Uniref for annotating metagenomic short reads as its running speed can guarantee a good annotation rate. This study may serve as a useful reference for selecting methods for Shellfish viral metagenome library construction and read annotation.
Zheng Tan,Wei-hui Zhong,Bao Meng,Shi-chao Duan,Hong-chen Wang3,Xing-You Yao,Yu-hui Zheng 국제구조공학회 2023 Steel and Composite Structures, An International J Vol.47 No.2
The bearing capacities resisted by the two-bay beams of multi-story planar frames with unequal spans under column removal scenarios differ considerably owing to the asymmetric stress on the left and right beams connected to the failed column and cause the potential for beams with larger span-to-depth ratios to be unable to exert effectively, which is disadvantageous for resisting the vertical load in unequal-span frame structures. To address this problem, the structural measure of adding braces to the weak bays of multi-story unequal-span frames was proposed, with the objective of achieving a coordinated stress state in two-bay beams with unequal spans, thereby improving the collapse resistance of unequal-span frame structures. Before conducting the numerical simulation, the modeling methods were verified by previous experimental results of two multi-story planar frames with and without steel braces. Thereafter, the effects of the tensile and compressive braces on the collapse behavior of the frame structures were elucidated. Then, based on the mechanical action laws of the braces throughout the collapse process, a detailed design method for improving the collapse resistance of unequal-span frame structures was proposed. Finally, the proposed design method was verified by using sufficient example models, and the results demonstrated that the design method has good application prospects and high practical value.
( Xing Wei Wang ),( Wei Wei ),( Wei Qiang Wang ),( Xiao Yan Zhao ),( Hong Guo ),( Dian Chun Fang ) 대한소화기학회 2014 Gut and Liver Vol.8 No.5
Background/Aims: To investigate the differential expression of RING finger (RNF) proteins in Barrett esophagus (BE) and esophageal adenocarcinoma (EAC). Methods: The differential expression of RNFs in normal esophagus (NE), BE, and EAC was screened using microarray assay. Real-time quantitative polymerase chain reaction (PCR), tissue microarray assay, and Western blot analysis were independently performed to detect the mRNA and protein expression of screened RNFs. Results: The expression of nine RNFs in the BE or EAC was 2-fold higher than those in NE. Among these proteins, the RNF32 and RNF121 expression in BE was 20.3-fold and 16.4-fold higher, respectively, than that in NE, and the expression of RNF24, RNF130, RNF141, RNF139, RNF11, RNF14, and RNF159 was upregulated more than 2-fold compared with NE. The expression of nine RNFs was not only upregulated in the EAC but was also positively related to the RNF expression in BE. The PCR results also indicated increased expression of these RNFs in BE and EAC compared to NE. Furthermore, the mRNA expression of all RNFs, except for RNF141 in EAC, was dramatically higher than those in the BE. Similar results were also obtained from the Western blot analysis. Conclusions: A total of nine RNFs play critical roles in the progression of BE to EAC. (Gut Liver 2014;8:487-494)
Bi, Wei-Wei,Zhang, Wei-Hua,Yin, Gui-Hua,Luo, Hong,Wang, Shou-Qin,Wang, Hongran,Li, Chao,Yan, Wei-Qun,Nie, De-Zhi Asian Pacific Journal of Cancer Prevention 2014 Asian Pacific journal of cancer prevention Vol.15 No.14
Background: To determine the amount of co-expression of IDO and EGFR in breast cancer patients. Materials and Methods:In order to obtain the distribution of co-expression of IDO and EGFR in breast cancer, we tested 110 breast cancer paraffin tissue blocks with immunohistochemical methods. Then we investigated the relationship between the diagnostic and pathologic characteristics (tumor size, lymph node status, histologic grade, the gene expression of ER, PR, HER2, p53, Ki67 and PCNA) with the situation of co-expression of IDO and EGFR by reviewing the medical records of 32 breast cancer patients. Results: Among 110 breast cancers, 32 cases demonstrated IDO and EGFR co-expression (29.1%), IDO and EGFR synchronous co-expression being found in 19.1% and asynchronous in 10.0%. Conclusions: IDO and EGFR were co-expressed in breast cancer, including synchronous and asynchronous co-expression. The results suggest that considering IDO and EGFR as two indicators for breast cancer treatment or prognosis analysis provides a potential option of individual treatment for the portion of breast cancer patients with co-expression of IDO and EGFR.
AlN with Strong Blue Emission Synthesized Through a Solventless Route
Wei Wang,Peng Zhang,Xiaobai Wang,Xiang Lei,Xiaodong Chen,Hong Ding,Hua Yang 성균관대학교(자연과학캠퍼스) 성균나노과학기술원 2016 NANO Vol.11 No.2
Aluminum nitride (AlN) with strong blue emission at 450 nm has been synthesized from hexahydrate aluminum chloride and urea above 850℃ via a solventless route. Several aluminum and nitrogen sources are selected and well investigated to determine the effect of AlN synthesis. Moreover, the structure, component, morphology, photoluminescence properties and possible synthesis mechanism are also discussed carefully.
Constituents from Zhuyeqing Liquor with hepatoprotective effect on alcohol-induced HepaG 2 toxicity
Hong-Ying Gao,Guo-Yu Li,Hang-Yu Wang,Jian Huang,Xiao-Wei Du,Ying Han,Li-Fei Wang,Jin-Hui Wang 대한약학회 2015 Archives of Pharmacal Research Vol.38 No.5
An unprecedented new skeleton compound (1R,10R, 11S)-10,11-dimethyl-4-formyl-2,9-dioxa-bicyclo [5.4.0]undeca-4,6-dien-3-one (1), monoterpenoids and monoterpeneglycoside picrocrocinic ester (2), epijasminoside B (3) and 60 -O-(3-methoxyl-4-hydroxyl-coumaroyl)-epijasminoside B (4),along with 26 known compounds, were obtained fromZhuyeqing Liquor. These compounds were identified mainlyby analyzing their NMR, HR-ESI–MS and CD data. The isolatedcompounds were screened against alcohol induced HepaG2 toxicity for hepatoprotective assay. Compounds 10, 19,21 and 26 displayed the highest potency against alcoholinduced HepaG 2 toxicity with the cell viability ratio 41.21,56.91, 67.69 and 70.32 % respectively.
DNA Microarray Probe Preparation by Gel Isolation Nested PCR
( Hong Min Wang ),( Wen Li Ma ),( Hai Huang ),( Wei Wei Xiao ),( Yan Wang ),( Wen Ling Zheng ) 생화학분자생물학회 2004 BMB Reports Vol.37 No.3
To develop a simplified method that can rapidly prepare DNA microarray probes in a massive scale, a lambda phage genomic DNA-fragments library was constructed for the microarray-probes collection. Four methods of DNA band recovery from the first PCR products were tested and compared. The DNA microarray probes were collected by a novel method of nested PCR that was mediated by gel isolation of the first PCR products. This method was named GIN-PCR. The probes that were prepared by this GIN-PCR technique were used as subjects to fabricate a DNA microarray. The results showed that a wooden toothpick was superior to the other 3 methods, since this technique can steadily transfer the DNA bands as the template of the second PCR after the first PCR. A group of probes were successfully collected and DNA microarrays were constructed using these probes. Hybridization results demonstrated that this technique of DNA recovery and probe preparation was rapid, efficient, and effective. We developed a cost-effective and less labor-intensive method for DNA microarray probe preparation by nested PCR that is mediated by wooden toothpick transfer of the DNA bands in the gel after electrophoresis.
Wang, Hong-Ping,Zhang, You-Bo,Yang, Xiu-Wei,Zhao, Da-Qing,Wang, Ying-Ping The Korean Society of Ginseng 2016 Journal of Ginseng Research Vol.40 No.4
Background: Ginsenosides are the characteristic and principal components which manifest a variety of the biological and pharmacological activities of the roots and rhizomes of Panax ginseng (GRR). This study was carried out to qualitatively and quantitatively determine the ginsenosides in the cultivated and forest GRR. Methods: A rapid and sensitive ultra-high-performance liquid chromatography coupled with diode-array detector and quadrupole/time of flight tandem mass spectrometry (UPLC-DAD-QTOF-MS/MS) was applied to the qualitative analysis of ginsenosides and a 4000 QTRAP triple quadrupole tandem mass spectrometer (HPLC-ESI-MS) was applied to quantitative analysis of 19 ginsenosides. Results: In the qualitative analysis, all ingredients were separated in 10 min. A total of 131 ginsenosides were detected in cultivated and forest GRR. The method for the quantitative determination was validated for linearity, precision, and limits of detection and quantification. 19 representative ginsenosides were quantitated. The total content of all 19 ginsenosides in the forest GRR were much higher than those in the cultivated GRR, and were increased with the growing ages. Conclusion: This newly developed analysis method could be applied to the quality assessment of GRR as well as the distinction between cultivated and forest GRR.
Wei-dong Wang,Li-hua Zhang,Jia-Yan Ni,Xiong-ying Jiang,Dong Chen,Yao-ting Chen,Hong-liang Sun,Jiang-hong Luo,Lin-feng Xu 대한영상의학회 2018 Korean Journal of Radiology Vol.19 No.4
Objective: To meta-analytically compare combined transarterial chemoembolization (TACE) plus radiofrequency ablation (RFA) and surgical resection (SR) for the treatment of hepatocellular carcinoma (HCC) within the Milan criteria. Materials and Methods: PubMed, Medline, Embase, and Cochrane Library were searched for studies comparing these two therapies that were published between January 2006 and August 2017. Overall survival rate (OS), recurrence-free survival rate (RFS), major complications and the average length of hospital stay were compared between these two therapies. Metaanalytic pooled odds ratio (OR) was calculated using TACE plus RFA as the base category. Results: Seven case-control studies and one randomized trial were identified. Meta-analytic results revealed that, compared with SR, TACE plus RFA had significantly higher 1-year OS (OR for survival = 0.50, p = 0.009) and lower major complications (OR = 1.88, p = 0.02) after therapy. Three studies reported on the length of hospital stay. The average length ± standard deviation reported in individual studies for SR and TACE plus RFA groups was 19.8 ± 8.4 days and 7.4 ± 2.2 days, respectively; 18.7 ± 4.9 days and 11.5 ± 6.9 days, respectively; and 16.6 ± 6.7 days and 8.5 ± 4.1 days, respectively (p < 0.0001 for all studies). Three or 5-year OS and 1-, 3-, or 5-year RFS did not significantly differ between the two therapies. Conclusion: Combined TACE plus RFA may be an alternative to SR for the treatment of patients with HCC within Milan the criteria. Non-randomized design in most of the original studies was a limitation.