| 1. |
- Huang, Jiaqi, et al.
(författare)
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Rapid Screening of Complex DNA Samples by Single-Molecule Amplification and Sequencing
- 2011
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Ingår i: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 6:5, s. e19723-
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Tidskriftsartikel (refereegranskat)abstract
- Microbial cloning makes Sanger sequencing of complex DNA samples possible but is labor intensive. We present a simple, rapid and robust method that enables laboratories without special equipment to perform single-molecule amplicon sequencing, although in a low-throughput manner, from sub-picogram quantities of DNA. The method can also be used for quick quality control of next-generation sequencing libraries, as was demonstrated for a metagenomic sample.
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| 2. |
- Li, W., et al.
(författare)
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On improvement of a conditional mornitoring technique for condition-based maintenance
- 2019
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Ingår i: International Conference on Nuclear Engineering, Proceedings, ICONE. - : ASME Press. - 9784888982566
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Konferensbidrag (refereegranskat)abstract
- The condition-based maintenance (CMB) is a hot research topic to overcome the drawbacks belonging to the periodic maintenance used in nuclear power plants nowadays. Auto-Associative Kernel Regression (AAKR) is a widely applied condition monitoring technique which is the basis of a CBM. In this paper, the traditional AAKR is improved by using the ensemble learning technique. The modified AAKR is tested by steady-state operational data of a Tennessee-Eastman chemical process and the results show that it can significantly improve the auto- and cross-sensitivity without reducing the accuracy. This indicates a significant improvement in performance of this condition monitoring technique.
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| 3. |
- Ndegwa, Nelson, et al.
(författare)
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Gastric Microbiota in a Low-Helicobacter pylori Prevalence General Population and Their Associations With Gastric Lesions
- 2020
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Ingår i: Clinical and Translational Gastroenterology. - : LIPPINCOTT WILLIAMS & WILKINS. - 2155-384X. ; 11
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Tidskriftsartikel (refereegranskat)abstract
- INTRODUCTION:Non-Helicobacter pylori microbiota might account for some cases with unexplained chronic gastritis that may in a minority eventually progress to gastric cancer through the Correa cascade. We characterized gastric microbiota by describing the normal stomach, compared it with early precancerous lesions and other disease states, and assessed whether H. pylori status affects bacterial diversity.METHODS:In a population-based study of those with and without gastrointestinal symptoms, cytology brush samples were collected during endoscopy from 316 individuals. Mucosal status was classified as normal mucosa (171), nonatrophic H. pylori gastritis (33), atrophic gastritis (12), or antral chemical gastritis (61). The 16S rRNA gene sequencing and analysis were performed to characterize the microbiota.RESULTS:Microbiota in atrophic gastritis and nonatrophic H. pylori gastritis stomachs were dysbiotic and differed from those in the normal stomach (P = 0.001). The normal stomach had the highest microbial diversity, followed by antral chemical gastritis. The atrophic gastritis and chronic H. pylori gastritis groups had the lowest diversity, a difference that was statistically significant (P = 0.01). Besides H. pylori, non-H. pylori bacteria accounted for group differences. Microbial network analysis showed that the normal group network was most highly connected, whereas the H. pylori gastritis group had the lowest connection. We found an increasing positive co-occurrence of oral bacteria in the stomach because samples deviated from the normal network, some of which were pathogens. The H. pylori-negative group had the highest microbial diversity (Shannon index) compared with the H. pylori-positive group (P = 0.001).DISCUSSION:In this low-H. pylori prevalence general population, the gastric mucosal microbiota of the normal stomach differed significantly from those with nonatrophic or atrophic gastritis. There was an increasing abundance of pathogenic bacteria from the normal state to early precancerous states.
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| 4. |
- Wang, Ke, et al.
(författare)
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Experimental Study on the Dynamics of a Thin Liquid Film under Shearing Force
- 2017
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Ingår i: Jixie Gongcheng Xuebao/Journal of Mechanical Engineering. - : Chinese Journal of Mechanical Engineering. - 0577-6686. ; 53:24, s. 70-76
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Tidskriftsartikel (refereegranskat)abstract
- The "scales-separation" phenomenon indicates that high heat-flux boiling and boiling crisis is dominated by micro-hydrodynamics of liquid microlayer on the heater surface. The techniques for liquid film measurement such as acoustic methods, nucleonic techniques, electrical methods, and optical methods are discussed in detail. Accordingly, a confocal optical sensor system is used to detect the dynamics of liquid film sheared by the co-flowing air from above in a horizontal aluminum channel. The impact of the gas shearing on film behaviors is analyzed and the integrity of liquid film is discussed in detail. The results indicate that the liquid film thickness decreases due to the entrainment and shows a linear or nonlinear variation under different flow conditions. Additionally, for a specific surface, the critical film thickness for an integral film is found to have no relation with the gas and liquid flow rates but the fluctuation of the liquid film increases with the increasing gas velocity.
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| 5. |
- Zheng, Zongli, et al.
(författare)
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A Method for Metagenomics of Helicobacter pylori from Archived Formalin-Fixed Gastric Biopsies Permitting Longitudinal Studies of Carcinogenic Risk
- 2011
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Ingår i: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 6:10, s. e26442-
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Tidskriftsartikel (refereegranskat)abstract
- The human microbiota has come into focus in the search for component causes of chronic diseases, such as gastrointestinal cancers. Presumably long induction periods and altered local environments after disease onset call for the development of methods for characterization of microorganisms colonizing the host decades before disease onset. Sequencing of microbial genomes in old formalin-fixed and paraffin-embedded (FFPE) gastrointestinal biopsies provides a means for such studies but is still challenging. Here we report a method based on laser capture micro-dissection and modified Roche 454 high-throughput pyrosequencing to obtain metagenomic profiles of Helicobacter pylori. We applied this method to two 15 year old FFPE biopsies from two patients. Frozen homogenized biopsies from the same gastroscopy sessions were also available for comparison after re-culture of H. pylori. For both patients, H. pylori DNA dissected from FFPE sections had similar to 96.4% identity with culture DNA from the same patients, while only similar to 92.5% identity with GenBank reference genomes, and with culture DNA from the other patient. About 82% and 60% of the predicted genes in the two genomes were captured by at least a single sequencing read. Along with sequences displaying high similarity to known H. pylori genes, novel and highly variant H. pylori sequences were identified in the FFPE sections by our physical enrichment approach, which would likely not have been detected by a sequence capture approach. The study demonstrates the feasibility of longitudinal metagenomic studies of H. pylori using decade-preserved FFPE biopsies.
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| 6. |
- Zheng, Zongli, et al.
(författare)
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Titration-free 454 sequencing using Y adapters
- 2011
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Ingår i: Nature Protocols. - : Springer Science and Business Media LLC. - 1754-2189 .- 1750-2799. ; 6:9, s. 1367-1376
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Tidskriftsartikel (refereegranskat)abstract
- We describe a protocol for construction and quantification of libraries for emulsion PCR (emPCR)-based sequencing platforms such as Roche 454 or Ion Torrent PGM. The protocol involves library construction using customized Y adapters, quantification using TaqMan-MGB (minor groove binder) probe-based quantitative PCR (qPCR) and calculation of an optimal template-to-bead ratio based on Poisson statistics, thereby avoiding the need for a laborious titration assay. Unlike other qPCR methods, the TaqMan-MGB probe specifically quantifies effective libraries in molar concentration and does not require specialized equipment. A single quality control step prior to emulsion PCR ensures that libraries contain no adapter dimers and have an optimal length distribution. The presented protocol takes similar to 7 h to prepare eight barcoded libraries from genomic DNA into libraries that are ready to use for full-scale emPCR. It will be useful, for example, to allow analyses of precious clinical samples and amplification-free metatranscriptomics.
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