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| 1 | Design of 16S rRNA gene primers for 454 pyrosequencing of the human foregut microbiome显示文摘AIM:To design and validate broad-range 16S rRNA primers for use in high throughput sequencing to classify bacteria isolated from the human foregut microbiome.METHODS:A foregut microbiome dataset was constructed using 16S rRNA gene sequences obtained from oral,esophageal,and gastric microbiomes produced by Sanger sequencing in previous studies represented by 219 bacterial species.Candidate primers evaluated were from the European rRNA database.To assess the effect of sequence length on accuracy of classification,16S rRNA genes of various lengths were created by trimming the full length sequences.Sequences spanning various hypervariable regions were selected to simulate the amplicons that would be obtained using possible primer pairs.The sequences were compared with full length 16S rRNA genes for accuracy in taxonomic classification using online software at the Ribosomal Database Project (RDP).The universality of the primer set was evaluated using the RDP 16S rRNA database which is comprised of 433 306 16S rRNA genes,represented by 36 phyla.RESULTS:Truncation to 100 nucleotides(nt)downstream from the position corresponding to base 28 in the Escherichia coli 16S rRNA gene caused misclassification of 87(39.7%)of the 219 sequences,compared with misclassification of only 29(13.2%)sequences with truncation to 350 nt.Among 350-nt sequence reads within various regions of the 16S rRNA gene,the reverse read of an amplicon generated using the 343F/798R primers had the least(8.2%)effect on classification.In comparison,truncation to 900 nt mimicking single pass Sanger reads misclassified 5.0%of the 219 sequences.The 343F/798R amplicon accurately assigned 91.8%of the 219 sequences at the species level.Weighted by abundance of the species in the esophageal dataset,the 343F/798R amplicon yielded similar classification accuracy without a significant loss in species coverage(92%).Modification of the 343F/798R primers to 347F/803R increased their universality among foregut species.Assuming that a typicalpolymerase chain reaction can tolerate 2 mismatches between a primer and a template,the modified 347F and 803R primers should be able to anneal 98%and 99.6%of all 16S rRNA genes in the RDP database.CONCLUSION:347F/803R is the most suitable pair of primers for classification of foregut 16S rRNA genes but also possess universality suitable for analyses of other complex microbiomes. | Carlos W Nossa William E Oberdorf Jφrn A Aas Bruce J Paster Todd Z DeSantis Eoin L Brodie Daniel Malamud Michael A Poles Zhiheng Pei | 2010 | World Journal of Gastroenterology2010，16，33： | 16 |
| 2 | Bacterial biota in reflux esophagitis and Barrett's esophagus显示文摘AIM: To identify the bacterial flora in conditions such as Barrett's esophagus and reflux esophagitis to determine if they are similar to normal esophageal flora.METHODS: Using broad-range 16S rDNA PCR,esophageal biopsies were examined from 24 patients [9with normal esophageal mucosa, 12 with gastroesophageal reflux disease (GERD), and 3 with Barrett's esophagus].Two separate broad-range PCR reactions were performed for each patient, and the resulting products were cloned.In one patient with Barrett's esophagus, g9 PCR clones were analyzed.RESULTS: Two separate clones were recovered from each patient (total = 48), representing 24 different species, with 14 species homologous to known bacteria,5 homologous to unidentified bacteria, and 5 were not homologous (<97% identity) to any known bacterial 16S rDNA sequences. Seventeen species were found in the reflux esophagitis patients, 5 in the Barrett's esophagus patients, and 10 in normal esophagus patients.Further analysis concentrating on a single biopsy from an individual with Barrett's esophagus revealed the presence of 21. distinct bacterial species. Members of four phyla were represented, including Bacteroidetes,Firmicutes, Proteobacteria, and Actinobacteria.Microscopic examination of each biopsy demonstrated bacteria in intimate association with the distal esophageal epithelium, suggesting that the presence of these bacteria is not transitory.CONCLUSION: These findings provide evidence for a complex, residential bacterial population in esophageal reflux-related disorders. While much of this biota is present in the normal esophagus, more detailed comparisons may help identify potential disease associations. | Zhiheng Pei Liying Yang Richard M Peek Jr Steven M Levine David T Pride Martin J Blaser | 2005 | World Journal of Gastroenterology2005，11，46： | 11 |
| 3 | NEAT1-TFE3和KAT6A-TFE3肾细胞癌:MiT家族易位性肾细胞癌中的新成员显示文摘小眼畸型相关转录因子(MiT)家族易位性肾细胞癌涉及TFE3或TFEB基因在内不同的基因融合。 据报道,TFE3的5′端可有多种融合基因伴侣,包括ASPSCR1、CLTC、DVL2、LUC7L3、KHSRP、PRCC、PARP14、NONO、SFPQ1、MED15以及RBM10。 通过免疫组化染色可以检测到这些融合基因激活TFE3转录。作者采用靶向RNA测序技术,鉴定了5例TFE3免疫组化染色阳性肾细胞癌的TFE3融合基因伴侣。3例为已知的基因融合,分别为ASPSCR1-TFE3、MED15-TFE3和RBM10-TFE3。2例为尚未报道的NEAT1-TFE3和KAT6A-TFE3基因融合。 | Pei J Cooper H Flieder D B 魏建国(摘译) 袁晓露(审校) | 2019 | 临床与实验病理学杂志2019，35，8： | 10 |
| 4 | Rhubarb extract partially improves mucosal integrity in chemotherapy-induced intestinal mucositis显示文摘AIM To investigate the effects of orally gavaged aqueous rhubarb extract(RE) on 5-fluorouracil(5-FU)-induced intestinal mucositis in rats. METHODS Female Dark Agouti rats(n = 8/group) were gavaged daily(1 mL) with water, high-dose RE(HDR; 200 mg/kg) or low-dose RE(LDR; 20mg/kg) for eight days. Intestinal mucositis was induced(day 5) with 5-FU(150 mg/kg) via intraperitoneal injection. Intestinal tissue samples were collected for myeloperoxidase(MPO) activity and histological examination. Xenopus oocytes expressing aquaporin 4 water channels were prepared to examine the effect of aqueous RE on cell volume, indicating a potential mechanism responsible for modulating net fluid absorption and secretion in the gastrointestinal tract. Statistical significance was assumed at P < 0.05 by one-way ANOVA. RESULTS B o d y w e i g h t w a s s i g n i f i c a n t l y r e d u c e d i n r a t s administered 5-FU compared to healthy controls(P < 0.01). Rats administered 5-FU significantly increased intestinal MPO levels(≥ 307%; P < 0.001), compared to healthy controls. However, LDR attenuated this effect in 5-FU treated rats, significantly decreasing ileal MPO activity(by 45%; P < 0.05), as compared to 5-FU controls. 5-FU significantly reduced intestinal mucosal thickness(by ≥ 29% P < 0.001) as compared to healthy controls. LDR significantly increased ileal mucosal thickness in 5-FU treated rats(19%; P < 0.05) relative to 5-FU controls. In xenopus oocytes expressing AQP4 water channels, RE selectively blocked water influx into the cell, induced by a decrease in external osmotic pressure. As water efflux was unaltered by the presence of extracellular RE, the directional flow of water across the epithelial barrier, in the presence of extracellular RE, indicated that RE may alleviate water loss across the epithelial barrier and promote intestinal health in chemotherapy-induced intestinal mucositis.CONCLUSION In summary, low dose RE improves selected parameters of mucosal integrity and reduces ileal inflammation, manifesting from 5-FU-induced intestinal mucositis. | Juliana E Bajic Georgina L Eden Lorrinne S Lampton Ker Y Cheah Kerry A Lymn Jinxin V Pei Andrea J Yool Gordon S Howarth | 2016 | World Journal of Gastroenterology2016，22，37： | 3 |
| 5 | Laser-induced microjet-assisted ablation for high-quality microfabrication显示文摘Liquid-assisted laser ablation has the advantage of relieving thermal effects of common laser ablation processes, whereas the light scattering and shielding effects by laser-induced cavitation bubbles, suspended debris, and turbulent liquid flow generally deteriorate laser beam transmission stability, leading to low energy efficiency and poor surface quality. Here, we report that a continuous and directional high-speed microjet will form in the laser ablation zone if laser-induced primary cavitation bubbles asymmetrically collapse sequentially near the air-liquid interface under a critical thin liquid layer. The laser-induced microjet can instantaneously and directionally remove secondary bubbles and ablation debris around the laser ablation region, and thus a very stable material removal process can be obtained. The shadowgraphs of high-speed camera reveal that the average speed of laser-induced continuous microjet can be as high as 1.1 m sin its initial 500 μm displacement. The coupling effect of laser ablation, mechanical impact along with the collapse of cavitation bubbles and flushing of high-speed microjet helps achieve a high material removal rate and significantly improved surface quality. We name this uncovered liquid-assisted laser ablation process as laser-induced microjet-assisted ablation(LIMJAA) based on its unique characteristics. High-quality microgrooves with a large depth-to-width ratio of 5.2 are obtained by LIMJAA with a single-pass laser scanning process in our experiments. LIMJAA is capable of machining various types of difficult-to-process materials with high-quality arrays of micro-channels, square and circle microscale through-holes. The results and disclosed mechanisms in our work provide a deep understanding of the role of laser-induced microjet in improving the processing quality of liquid-assisted laser micromachining. | Yang Guo Pei Qiu Shaolin Xu Gary J Cheng | 2022 | International Journal of Extreme Manufacturing2022，4，3： | 3 |
| 6 | The valence change from RE3+ (RE=Eu,Sm,Yb) in SrB4O7:RE prepared in air and the spectral properties of RE2+显示文摘 | PEI Z W SU Q ZHANG J Y | 1993 | Journal of Alloys and Compound1993，198，： | 2 |
| 7 | Efficient blue polymer light-emitting diodes from a series of soluble poly (paraphenylene)s显示文摘 | Yang Y Pei Q Heeger A J | 1996 | J Appl Phys1996，79，： | 2 |
| 8 | The evolution of microstructure in a laser clad TiB-Ti composite coating 显示文摘 | KOOI B J PEI Y T DE HOSSON J Th M | 2003 | Acta Mater2003，51，2： | 2 |
| 9 | Integration of the metabolome and transcriptome reveals the metabolites and genes related to nutritional and medicinal value in Coriandrum sativum显示文摘Coriandrum sativum(Coriander) or Chinese parsley is a culinary herb with multiple medicinal effects, which is widely used in cooking and traditional medicine. It is enriched with essential oils and anti-oxidant compounds with unknown significance. To explore the untapped reservoir of Coriander, we studied the transcriptome and metabolic profiles from three developmental stages. Here, we identified 10 tyrosine metabolic pathway-related genes(TMPRGs), six porphyrins and chlorophyll metabolic pathway-related genes(PCMPRGs), and five Vitamin E metabolic pathway-related genes(VEMPRGs). These genes were associated with the early development of Coriander. Our analysis suggests that these pathways are involved in the production of critical phenolic metabolites. Furthermore, we constructed the interaction network between these pathway-related genes and transcription factors(TFs), which supported the regulatory pathways for phenolic metabolites. Interestingly, we identified several nutritional or medicinally relevant metabolites, including 59 phenols, two polyamines, 12 alkaloids, and one terpenoid. The higher concentrations of metabolites were from caffeic acid, agmatine, and its derivatives. We found higher levels of caffeic acid and agmatine at 30 days compared to 60 or 90 days. This study provides evidence to stimulate further investigation of the role of these metabolites in medicinal and nutritional research. | WU Tong FENG Shu-yan YANG Qi-hang Preetida J BHETARIYA GONG Ke CUI Chun-lin SONG Jie PING Xiao-rui PEI Qiao-ying YU Tong SONG Xiao-ming | 2021 | Journal of Integrative Agriculture2021，20，7： | 2 |
| 10 | Polymer-enhance diffraction in an azo-dye-doped li-quid crystal显示文摘 | Pei M L Wang Y J Carlisle O O | 2001 | Society of Photo-Optical Instrumentation Engineers2001，40，8： | 1 |
| 11 | Cytotoxic T lymphocytes are critical in control of infectious bronchitis virus in poultry 显示文摘 | Collission E W Pei J Dzielawa J | 2000 | Develop Comp Immunol2000，24，23： | 1 |
| 12 | Memory T cells protect chicks from acute bronchitis virus infection显示文摘 | Pei J Briles WE collisson EW | 2003 | Virology 20032003，20，： | 1 |
| 13 | Synthesis and Characterization of V-HMS Employed for Catalytic Hydroxylation of Benzene 显示文摘 | Feng S J Pei S P Yue B | 2009 | Catal Lett2009，131，： | 1 |
| 14 | 查看详情显示文摘 | Li J Xie W X Pei J H | | 0，，5： | 1 |
| 15 | Efficient skyline and Top-k retrieval in subspaces 显示文摘 | TAO Y XIAO X PEI J | 2007 | IEEE Transactions on Knowledge and Data Engi- neering2007，19，8： | 1 |
| 16 | Investigation of gene effects and epistatic interactions between Aktl and neuregulin 1 in the regula- tion of behavioral phenotypes and social functions in genetic mouse models of schizophrenia显示文摘 | Huang C Pei J Luo D | 2014 | Front Behav Neurosci2014，8，： | 1 |
| 17 | Rotary Ultrasonic Machining of Structural Ceramics-A Review显示文摘 | Pei Z J Khanna N Ferreira P M | 1995 | Ceramic Engineering and Science Proceedings1995，，16： | 1 |
| 18 | An MAGDM approach combining numerical values with uncertain linguistic information and its appli- cation in evaluation of Rb-D projects显示文摘 | Liu X B Pei F Yang J B | 2010 | International Journal of Computational Intelligence Systems2010，3，5： | 1 |
| 19 | Top-k typicality queries and efficient query answering methods on large databases显示文摘 | Hua M Pei J Fu A W C | 2009 | The International Journal on Very Large Data Bases(VLDB)2009，32，18： | 1 |
| 20 | κ-opioid receptor mediates cardioprotection of ischemic preconditioning role of PKC and KATP显示文摘 | WANG G Y W U S PEI J M | 2001 | Am J Physiol2001，280，： | 1 |
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