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2. Methodologies for 176Lu-176Hf Analysis of Zircon Grains from the Moon and Beyond

Author

Chen, Xi, Dauphas, Nicolas, Zhang, Zhe J., Schoene, Blair, Barboni, Melanie, Leya, Ingo, Zhang, Junjun, Szymanowski, Dawid, and McKeegan, Kevin D.

Subjects
Astrophysics - Earth and Planetary Astrophysics
Abstract

Zircons are found in extraterrestrial rocks from the Moon, Mars, and some differentiated meteorite parent-bodies. These zircons are rare, often of small size, and have been affected by neutron capture induced by cosmic ray exposure. The application of the 176Lu-176Hf decay system to zircons from planetary bodies such as the Moon can help establish the chronology of large-scale differentiation processes, like the crystallization of the lunar magma ocean. Here, we present methods to measure the isotopic composition of Hf of extraterrestrial zircons dated using ID-TIMS U-Pb after chemical abrasion. We introduce a 2-stage elution scheme to separate Hf from Zr while preserving the unused Zr fraction for future isotopic analysis. The effect of neutron capture is also re-examined using the latest thermal neutron capture cross sections and epithermal resonance integrals. Our tests show that the precision of Hf isotopic analyses is close to what is theoretically attainable. We have tested this method to a limited set of zircon grains from lunar rocks returned by the Apollo missions (lunar soil 14163, fragmental polymict breccia 72275, and clast-rich breccia 14321). The model ages align with previously reported values, but further work is needed to assess the chronology of lunar magma ocean crystallization as only a handful of small zircons (5 zircons from 3 samples) were analyzed, and the precision of the analyses can be improved by measuring more and larger lunar zircon grains., Comment: ACS Earth and Space Chemistry, in press

Published
2023
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4. Research on Network Security Application Based on Data Mining Algorithm

Author

Zhang, JunJun, Li, Qian, Angrisani, Leopoldo, Series Editor, Arteaga, Marco, Series Editor, Chakraborty, Samarjit, Series Editor, Chen, Shanben, Series Editor, Chen, Tan Kay, Series Editor, Dillmann, Rüdiger, Series Editor, Duan, Haibin, Series Editor, Ferrari, Gianluigi, Series Editor, Ferre, Manuel, Series Editor, Hirche, Sandra, Series Editor, Jabbari, Faryar, Series Editor, Jia, Limin, Series Editor, Kacprzyk, Janusz, Series Editor, Khamis, Alaa, Series Editor, Kroeger, Torsten, Series Editor, Li, Yong, Series Editor, Liang, Qilian, Series Editor, Martín, Ferran, Series Editor, Ming, Tan Cher, Series Editor, Minker, Wolfgang, Series Editor, Misra, Pradeep, Series Editor, Mukhopadhyay, Subhas, Series Editor, Ning, Cun-Zheng, Series Editor, Nishida, Toyoaki, Series Editor, Oneto, Luca, Series Editor, Panigrahi, Bijaya Ketan, Series Editor, Pascucci, Federica, Series Editor, Qin, Yong, Series Editor, Seng, Gan Woon, Series Editor, Speidel, Joachim, Series Editor, Veiga, Germano, Series Editor, Wu, Haitao, Series Editor, Zamboni, Walter, Series Editor, Tan, Kay Chen, Series Editor, Pei, Yan, editor, Ma, Hao Shang, editor, Chan, Yu-Wei, editor, and Jeong, Hwa-Young, editor

Published
2024
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8. JBrowse 2: a modular genome browser with views of synteny and structural variation

Author

Diesh, Colin, Stevens, Garrett J, Xie, Peter, De Jesus Martinez, Teresa, Hershberg, Elliot A, Leung, Angel, Guo, Emma, Dider, Shihab, Zhang, Junjun, Bridge, Caroline, Hogue, Gregory, Duncan, Andrew, Morgan, Matthew, Flores, Tia, Bimber, Benjamin N, Haw, Robin, Cain, Scott, Buels, Robert M, Stein, Lincoln D, and Holmes, Ian H

Subjects
Information and Computing Sciences, Biological Sciences, Genetics, Bioengineering, Human Genome, Generic health relevance, Genomics, Software, Synteny, Genome, Biological Evolution, Web Browser, Internet, Environmental Sciences, Bioinformatics
Abstract

We present JBrowse 2, a general-purpose genome annotation browser offering enhanced visualization of complex structural variation and evolutionary relationships. It retains core features of JBrowse while adding new views for synteny, dotplots, breakpoints, gene fusions, and whole-genome overviews. It allows users to share sessions, open multiple genomes, and navigate between views. It can be embedded in a web page, used as a standalone application, or run from Jupyter notebooks or R sessions. These improvements are enabled by a ground-up redesign using modern web technology. We describe application functionality, use cases, performance benchmarks, and implementation notes for web administrators and developers.

Published
2023

10. Analysis of genomic characteristics,antimicrobial and pathogenic genes of Listeria monocytogens in commercial food in Xianyang City

Author

ZHANG Junjun, ZHANG Guochao, WANG Yingying, YANG Nan, WANG Lijuan, LIU Gang, and QIN Long

Subjects
listeria monocytogenes, whole genome sequencing, antimicrobial, virulence, Food processing and manufacture, TP368-456, Nutrition. Foods and food supply, TX341-641
Abstract

ObjectiveTo use whole genome sequencing （WGS） to analysis the genomic characteristics， the antimicrobial resistance and virulence genotypes of 64 Listeria monocytogenes strains isolated from commercial food in Xianyang City.MethodsSixty four Listeria monocytogenes were isolated and the susceptibilities were determined by broth microdilution. After the whole genome sequencing， using bioinformatics software for genome annotation， phylogenetic tree construction， genome features and genetic components analysis.ResultsAll isolates were found to be susceptible to ampicillin， Penicillin， meropenem， trimethoprim-sulfamethoxazole， vancomycin. 2 isolates were resistant to tetracycline and erythromycin at the same time. All isotates were categorized into three different lineages and 15 CCs， Lineage Ⅰ and Ⅱ were the predominant types. The genotypes of 2 resistant isolates correlated well with its resistant phenotype. Up and down stream analysis of the genetic context， in which these resistant genes were found， suggested that they may have been acquired from Erysipelothrix rhusiopathiae， Enterococcus and plasmid. All the isolates harboured the LIPI-1 and LIPI-2， subset of lineage Ⅰ isotates harboured LIPI-3 or LIPI-4 with potential pathogenicity. Lineage Ⅱ isotates harboured more plasmids and genes linked to stress adaptation . The premature stop codon （PMSC） mutation in inlA more frequently happened in lineage Ⅱ and may reduce virulence.ConclusionThe genome of Listeria monocytogenes in commercial food in Xianyang City is stable. Acquires resistance existed in this bacterium， and can be a potential public health risk due to its high harboring rate of virulence genes. Lineage Ⅰ and Lineage Ⅱ isolates were differ in virulence genes， stress adaptation genes and plasmids harboring， indicating differences among subtypes. This findings would be helpful to the surveillance and control of this foodborne pathogen in Xianyang City.

Published
2024
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35. Development and Application of Visual Freshness Indicator Film with High Stability Based on Acylated Anthocyanins

Author

ZHANG Junjun, ZOU Xiaobo, SONG Wenjun, DU Liuzi, SHI Jiyong, HUANG Xiaowei, ZHANG Jianing, LI Zhihua, LIU Li

Subjects
acylated roselle anthocyanins, stability, beef freshness, intelligent indicator film, sensitivity, Food processing and manufacture, TP368-456
Abstract

Roselle anthocyanins were acylated and acylated anthocyanins with higher thermal and light stability were obtained. Then, a smart indicator film was prepared using polyvinyl alcohol and β-cyclodextrin as film-forming substrates and acylated anthocyanins as an indicator. Its mechanical properties, color response sensitivity and stability were investigated. The tensile strength of polyvinyl alcohol/β-cyclodextrin/acylated roselle anthocyanin (PCRA) film was more than three times as high as that of polyvinyl alcohol/β-cyclodextrin/roselle anthocyanin (PCR) film, and the microstructure of the PCRA film was more compact. In addition, the water vapor transmittance of the PCRA film was 2.06 × 10-6 g/(m·h·Pa) and higher than that of the PCR film. The stability of the PCRA film was higher while the color response sensitivity was lower. Then, the PRCA film was applied as an indicator for monitoring beef freshness at 4 ℃. The total volatile base nitrogen (TVB-N) content of beef increased to 16.81 mg/100 g on the sixth day of storage, indicating that the beef was spoiled. The color of the PCRA film changed from pink to yellow-green, which could effectively reflect the freshness of beef. Finally, we found a high correlation coefficient between the physicochemical information of beef and the color information of the indicator film, further confirming that the visual film can be applied to monitor beef freshness. The results of this study provide a basis for the development of intelligent food packaging in the future.

Published
2023
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45. Separation Effect of Early Visual Cortex V1 Under Different Crowding Conditions A TMS Study

Author

Liu, Xieyi, Zhang, Junjun, and Li, Ling

Subjects
Quantitative Biology - Neurons and Cognition
Abstract

The visual crowding makes it difficult to identify the patterns in peripheral vision, but the neural mechanism for this phenomenon is still unclear because of different opinions. In order to study the separation effect of V1 under different crowding conditions, single-pulse transcranial magnetic stimulation is applied within the right V1. The experimental design includes two factors: TMS intensity (10%, 65%, and 90% of the phosphene threshold) and crowding (high and low) conditions. The accuracy results show that there is a strong interaction between crowding condition and TMS condition. When the TMS stimulation intensity is lower than the phosphene threshold, more crowding will be perceived under the high crowding condition, and less crowding will be perceived under the low crowding condition. The above results conclude that the high and low crowding condition separate by TMS stimulation. The results support the assumption that the crowding is related to V1 and occurs in the visual coding phase.

Published
2019

50. A user guide for the online exploration and visualization of PCAWG data.

Author

Goldman, Mary J, Zhang, Junjun, Fonseca, Nuno A, Cortés-Ciriano, Isidro, Xiang, Qian, Craft, Brian, Piñeiro-Yáñez, Elena, O'Connor, Brian D, Bazant, Wojciech, Barrera, Elisabet, Muñoz-Pomer, Alfonso, Petryszak, Robert, Füllgrabe, Anja, Al-Shahrour, Fatima, Keays, Maria, Haussler, David, Weinstein, John N, Huber, Wolfgang, Valencia, Alfonso, Park, Peter J, Papatheodorou, Irene, Zhu, Jingchun, Ferretti, Vincent, and Vazquez, Miguel

Subjects
Humans, Neoplasms, Computational Biology, Genomics, Mutation, Genome, Human, Internet, Software, User-Computer Interface, Databases, Genetic, Chromothripsis, Whole Genome Sequencing, Data Analysis, Genome, Human, Databases, Genetic
Abstract

The Pan-Cancer Analysis of Whole Genomes (PCAWG) project generated a vast amount of whole-genome cancer sequencing resource data. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2658 cancers across 38 tumor types, we provide a user's guide to the five publicly available online data exploration and visualization tools introduced in the PCAWG marker paper. These tools are ICGC Data Portal, UCSC Xena, Chromothripsis Explorer, Expression Atlas, and PCAWG-Scout. We detail use cases and analyses for each tool, show how they incorporate outside resources from the larger genomics ecosystem, and demonstrate how the tools can be used together to understand the biology of cancers more deeply. Together, the tools enable researchers to query the complex genomic PCAWG data dynamically and integrate external information, enabling and enhancing interpretation.

Published
2020

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