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6. Genomic signatures of past and present chromosomal instability in Barrett’s esophagus and early esophageal adenocarcinoma

Author

Bao, Chunyang, Tourdot, Richard W, Brunette, Gregory J, Stewart, Chip, Sun, Lili, Baba, Hideo, Watanabe, Masayuki, Agoston, Agoston T, Jajoo, Kunal, Davison, Jon M, Nason, Katie S, Getz, Gad, Wang, Kenneth K, Imamura, Yu, Odze, Robert, Bass, Adam J, Stachler, Matthew D, and Zhang, Cheng-Zhong

Subjects
Biological Sciences, Biomedical and Clinical Sciences, Oncology and Carcinogenesis, Genetics, Human Genome, Rare Diseases, Cancer, Digestive Diseases, 2.1 Biological and endogenous factors, Aetiology, Humans, Barrett Esophagus, Esophageal Neoplasms, Adenocarcinoma, Chromosomal Instability, Precancerous Conditions, Genomics, Disease Progression
Abstract

The progression of precancerous lesions to malignancy is often accompanied by increasing complexity of chromosomal alterations but how these alterations arise is poorly understood. Here we perform haplotype-specific analysis of chromosomal copy-number evolution in the progression of Barrett's esophagus (BE) to esophageal adenocarcinoma (EAC) on multiregional whole-genome sequencing data of BE with dysplasia and microscopic EAC foci. We identify distinct patterns of copy-number evolution indicating multigenerational chromosomal instability that is initiated by cell division errors but propagated only after p53 loss. While abnormal mitosis, including whole-genome duplication, underlies chromosomal copy-number changes, segmental alterations display signatures of successive breakage-fusion-bridge cycles and chromothripsis of unstable dicentric chromosomes. Our analysis elucidates how multigenerational chromosomal instability generates copy-number variation in BE cells, precipitates complex alterations including DNA amplifications, and promotes their independent clonal expansion and transformation. In particular, we suggest sloping copy-number variation as a signature of ongoing chromosomal instability that precedes copy-number complexity. These findings suggest copy-number heterogeneity in advanced cancers originates from chromosomal instability in precancerous cells and such instability may be identified from the presence of sloping copy-number variation in bulk sequencing data.

Published
2023

15. Short-Term Industrial Load Forecasting Based on VMD-KELM-Xgboost

Author

Wu, Jingying, Zhou, Xiang, Sun, Lili, Jin, Luosong, 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, 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, Chen, Zhe, editor, Yang, Wenming, editor, and Chen, Hao, editor

Published
2024
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16. Truncated Order Reduction Methods for Discrete Linear Periodic Time-Varying Systems

Author

Sun, Lili, Chen, Jun, Zhang, Xuedong, Meng, Hongbing, 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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17. Joint Security Protection and Transmission Delay Scheduling Scheme of Voice Switching Network

Author

Tang, Ruilin, Zhai, Hongting, Zhai, Qi, Zhang, Yantong, Bian, Ruochen, Sun, Lili, Zhang, Qingrui, Quan, Weihong, He, Xinxin, Angrisani, Leopoldo, Series Editor, Arteaga, Marco, Series Editor, Chakraborty, Samarjit, Series Editor, Chen, Jiming, 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, 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, Zhang, Junjie James, Series Editor, Tan, Kay Chen, Series Editor, Wang, Wei, editor, Mu, Jiasong, editor, Liu, Xin, editor, and Na, Zhenyu Na, editor

Published
2024
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18. A Multidimensional Detection Model of Android Malicious Applications Based on Dynamic and Static Analysis

Author

Zhang, Hao, Liu, Donglan, Liu, Xin, Ma, Lei, Wang, Rui, Zhang, Fangzhe, Sun, Lili, Zhao, Fuhui, Angrisani, Leopoldo, Series Editor, Arteaga, Marco, Series Editor, Chakraborty, Samarjit, Series Editor, Chen, Jiming, 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, 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, Zhang, Junjie James, Series Editor, Tan, Kay Chen, Series Editor, Zhang, Yonghong, editor, Qi, Lianyong, editor, Liu, Qi, editor, Yin, Guangqiang, editor, and Liu, Xiaodong, editor

Published
2024
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40. Dual targeted extracellular vesicles regulate oncogenic genes in advanced pancreatic cancer

Author

Chiang, Chi-Ling, Ma, Yifan, Hou, Ya-Chin, Pan, Junjie, Chen, Sin-Yu, Chien, Ming-Hsien, Zhang, Zhi-Xuan, Hsu, Wei-Hsiang, Wang, Xinyu, Zhang, Jingjing, Li, Hong, Sun, Lili, Fallen, Shannon, Lee, Inyoul, Chen, Xing-Yu, Chu, Yeh-Shiu, Zhang, Chi, Cheng, Tai-Shan, Jiang, Wen, Kim, Betty Y. S., Reategui, Eduardo, Lee, Robert, Yuan, Yuan, Liu, Hsiao-Chun, Wang, Kai, Hsiao, Michael, Huang, Chi-Ying F., Shan, Yan-Shen, Lee, Andrew S., and James Lee, L.

Published
2023
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49. Influencing Factors of Scientific Data Value Increment Based on System Dynamics

Author

SUN Lili, WANG WeiJie, SHENG Jiefei

Subjects
scientific data, value increment, influencing factors, system dynamics, data elements, fair, Bibliography. Library science. Information resources, Agriculture
Abstract

[Purpose/Significance] To explore the influencing factors of the added value of scientific data and reveal the inherent development laws of the added value of scientific data. [Method/Process] First, based on the interview data of 18 experts and the research results related to the value appreciation of scientific data in existing literature, the grounded theory method was adopted. Through open coding, main-axis coding, and selective coding, 19 categories, 6 main categories, and 3 core categories were finally obtained. From this, a theoretical model of the factors influencing the value appreciation of scientific data was obtained. On this basis, the Vensim PLE tool was used to establish a dynamic model of the value appreciation system of scientific data, and the process of value appreciation of scientific data was dynamically simulated and analyzed to reveal the relationship between various influencing factors and the value appreciation of scientific data. [Results/Conclusions] In the process of increasing the value of scientific data, the quality factor of raw data is a prerequisite, and high-quality raw scientific data are conducive to the integration and secondary development of subsequent scientific data. The data literacy of data producers represented by researchers has the most significant impact on the quality of scientific data. The level of data storage and payment has a significant impact on the added value of scientific data. When the perceived effort and perceived risk of data storage and payment by researchers decrease, accompanied by the pressure of scientific data sharing policies, researchers become more likely to increase their willingness to save and pay, thereby significantly improving the scale effect of data storage and payment. The organization and integration of scientific data is the key to the formation of value-added scientific data. Overall, the metadata quality has the most significant impact on the level of scientific data organization and integration. The quality of metadata is the foundation of scientific data processing, classification, and integration. The higher the quality of metadata, the more it helps to improve the level of scientific data organization and integration. The sharing and development of scientific data is the key to realizing the value-added of scientific data. It is the final step in realizing the value-added of scientific data. In this process, the scale of scientific data openness, the quality of scientific data sharing platforms, and development capabilities all have a positive promoting effect on the level of scientific data sharing and development.

Published
2023
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