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244 results on '"Yang, Yimeng"'

2. Reconstruction of 3D Fetal Brain MRI from 2D Cross-Sectional Acquisitions Using Unsupervised Learning Network

Author

Yang, Yimeng, Gu, Dongdong, Zhang, Xukun, Ding, Zhongxiang, Gao, Fei, Xue, Zhong, Shen, Dinggang, Goos, Gerhard, Founding Editor, Hartmanis, Juris, Founding Editor, Bertino, Elisa, Editorial Board Member, Gao, Wen, Editorial Board Member, Steffen, Bernhard, Editorial Board Member, Yung, Moti, Editorial Board Member, Cao, Xiaohuan, editor, Xu, Xuanang, editor, Rekik, Islem, editor, Cui, Zhiming, editor, and Ouyang, Xi, editor

Published
2024
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8. Superposed Wave (s-Wave): Accelerating Photoacoustic Simulation

Author

Zhang, Jiadong, Lyu, Tengbo, Yang, Changchun, Yang, Yimeng, Guo, Shanshan, Gao, Feng, and Gao, Fei

Subjects
Physics - Medical Physics
Abstract

Photoacoustic imaging develops very fast in recent years due to its superior performance in many preclinical and clinical applications. However, it is still in a developing stage, and a lot of experiments have to be performed in a simulation setting. To simulate photoacoustic imaging in a computer, k-Wave is currently the most popular MATLAB toolbox. Lots of research groups choose k-Wave toolbox to perform the forward projection process, which also can be described as forward model. However, by solving complex partial differential equation, k-Wave suffers a lot from computation time. To accelerate photoacoustic simulation, in this paper, we propose a straightforward simulation approach based on superposed Wave (s-Wave). Specifically, we treat the initial pressure distribution as a set of single pixels. Then by pre-obtaining a standard sensor data from single pixel, we can easily use loop and multiplication operators to change phase and amplitude of sensor data for given pixels. We use three different 2D samples and two 3D samples to test the time cost. The result of our proposed s-Wave method shows much less time consumption compared with k-wave. Especially in a sparse configuration in 3D, s-Wave is more than 2000 times faster than k-Wave, whiling getting nearly same sensor data.

Published
2020

10. EMPress Enables Tree-Guided, Interactive, and Exploratory Analyses of Multi-omic Data Sets

Author

Cantrell, Kalen, Fedarko, Marcus W, Rahman, Gibraan, McDonald, Daniel, Yang, Yimeng, Zaw, Thant, Gonzalez, Antonio, Janssen, Stefan, Estaki, Mehrbod, Haiminen, Niina, Beck, Kristen L, Zhu, Qiyun, Sayyari, Erfan, Morton, James T, Armstrong, George, Tripathi, Anupriya, Gauglitz, Julia M, Marotz, Clarisse, Matteson, Nathaniel L, Martino, Cameron, Sanders, Jon G, Carrieri, Anna Paola, Song, Jin, Swafford, Austin D, Dorrestein, Pieter C, Andersen, Kristian G, Parida, Laxmi, Kim, Ho-Cheol, Vázquez-Baeza, Yoshiki, and Knight, Rob

Subjects
Information and Computing Sciences, Graphics, Augmented Reality and Games, Biological Sciences, Human Genome, Genetics, bioinformatics, microbial ecology
Abstract

Standard workflows for analyzing microbiomes often include the creation and curation of phylogenetic trees. Here we present EMPress, an interactive web tool for visualizing trees in the context of microbiome, metabolome, and other community data scalable to trees with well over 500,000 nodes. EMPress provides novel functionality-including ordination integration and animations-alongside many standard tree visualization features and thus simplifies exploratory analyses of many forms of 'omic data.IMPORTANCE Phylogenetic trees are integral data structures for the analysis of microbial communities. Recent work has also shown the utility of trees constructed from certain metabolomic data sets, further highlighting their importance in microbiome research. The ever-growing scale of modern microbiome surveys has led to numerous challenges in visualizing these data. In this paper we used five diverse data sets to showcase the versatility and scalability of EMPress, an interactive web visualization tool. EMPress addresses the growing need for exploratory analysis tools that can accommodate large, complex multi-omic data sets.

Published
2021

12. Phylogenomics of 10,575 genomes reveals evolutionary proximity between domains Bacteria and Archaea.

Author

Zhu, Qiyun, Mai, Uyen, Pfeiffer, Wayne, Janssen, Stefan, Asnicar, Francesco, Sanders, Jon G, Belda-Ferre, Pedro, Al-Ghalith, Gabriel A, Kopylova, Evguenia, McDonald, Daniel, Kosciolek, Tomasz, Yin, John B, Huang, Shi, Salam, Nimaichand, Jiao, Jian-Yu, Wu, Zijun, Xu, Zhenjiang Z, Cantrell, Kalen, Yang, Yimeng, Sayyari, Erfan, Rabiee, Maryam, Morton, James T, Podell, Sheila, Knights, Dan, Li, Wen-Jun, Huttenhower, Curtis, Segata, Nicola, Smarr, Larry, Mirarab, Siavash, and Knight, Rob

Subjects
Bacteria, Archaea, Evolution, Molecular, Phylogeny, Genome, Bacterial, Genome, Archaeal
Abstract

Rapid growth of genome data provides opportunities for updating microbial evolutionary relationships, but this is challenged by the discordant evolution of individual genes. Here we build a reference phylogeny of 10,575 evenly-sampled bacterial and archaeal genomes, based on a comprehensive set of 381 markers, using multiple strategies. Our trees indicate remarkably closer evolutionary proximity between Archaea and Bacteria than previous estimates that were limited to fewer "core" genes, such as the ribosomal proteins. The robustness of the results was tested with respect to several variables, including taxon and site sampling, amino acid substitution heterogeneity and saturation, non-vertical evolution, and the impact of exclusion of candidate phyla radiation (CPR) taxa. Our results provide an updated view of domain-level relationships.

Published
2019

16. First Investigation on the Radiation Field of the Gas-Filled Three-Axis Cylindrical Hohlraum

Author

Li, Hang, Jing, Longfei, Jiang, Shaoen, Kuang, Longyu, Du, Huabin, Zhan, Xiayu, Li, Zhichao, Li, Sanwei, Li, Liling, Zheng, Jianhua, Zheng, Jinhua, Lin, Zhiwei, Zhang, Lu, Wang, Qiangqiang, Yang, Yimeng, Ma, Bo, Wang, Peng, Yang, Dong, Wang, Feng, Yang, Jiamin, Gao, Lin, Zhang, Haijun, Zhang, Juan, Wang, Honglian, Ye, Chenggang, Gu, Qianqian, Tang, Jie, Zhang, Wei, Xie, Jun, Yuan, Guanghui, He, Zhibing, Du, Kai, Chen, Xu, Huang, Xiaoxia, Wang, Yuancheng, Deng, Xuewei, Zhou, Wei, Wang, Liquan, Deng, Caibo, Ding, Yongkun, and Zhang, Baohan

Subjects
Physics - Plasma Physics
Abstract

A novel ignition hohlraum named three-axis cylindrical hohlraum (TACH) is designed for indirect-drive inertial confinement fusion. TACH is a kind of 6 laser entrance holes (LEHs) hohlraum, which is orthogonally jointed of three cylindrical hohlraums. The first experiment on the radiation field of TACH was performed on Shenguang III laser facility. 24 laser beams were elected and injected into 6 LEHs quasi-symmetrically. Total laser energy was about 59 kJ, and the peak radiation temperature reached about 192 eV. Radiation temperature and pinhole images in gas-filled hohlraum are largely identical but with minor differences with those in vacuum hohlraum. All laser energy can be totally delivered into hohlraum in 3 ns duration even without filled gas in the hohlraum of 1.4 mm diameter. Plasma filling cannot be obviously suppressed even with 0.5 atm pressure gas in the small hohlraum. Backscattering fractions of vacuum hohlraum and gas-filled hohlraum are both lower than 2%. Experimental study of this new kind of hohlraum can provide guidance for future target design and implosion experiment.

Published
2018

19. Measurement of 2p-3d absorption in a hot molybdenum plasma

Author

Xiong, Gang, primary, Qing, Bo, additional, Zhang, Zhiyu, additional, Jing, Longfei, additional, Zhao, Yang, additional, Wei, Minxi, additional, Yang, Yimeng, additional, Hou, Lifei, additional, Huang, Chengwu, additional, Zhu, Tuo, additional, Song, Tianming, additional, Lv, Min, additional, Zhao, Yan, additional, Zhang, Yuxue, additional, Yang, Guohong, additional, Wu, Zeqing, additional, Yan, Jun, additional, Zou, Yaming, additional, Zhang, Jiyan, additional, and Yang, Jiamin, additional

Published
2024
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37. Morphological and molecular characterisation of Rotylenchus astragalus sp. n. (Nematoda: Rhabditida: Hoplolaimidae) from Shanxi province, north China.

Author

Yin, Tian, Yang, Yimeng, Liu, Meina, Zhao, Zengqi, Wang, Jianming, and Xu, Yumei

Subjects
*ASTRAGALUS (Plants), *RHABDITIDA, *NEMATODES, *TWO-dimensional bar codes, *VULVA
Abstract

Summary: Rotylenchus astragalus sp. n. is characterised by having females 841-1069 μ m long, stylet 28-31 μ m long, basal knobs rounded, dorsal pharyngeal gland orifice (DGO) 3-5 μ m, lateral field with four incisures, pharyngeal gland lobes slender, overlapping intestine dorsally for 4-12 μ m, excretory pore located just posterior to the hemizonid, vulva slightly posterior to mid-body, ovaries paired, phasmid opening relatively large and 8-18 annuli anterior to the anus, tail conoid and absence of males. The matrix code of R. astragalus sp. n. is A5, B3, C1, D4, E1, F2, G1-2, H3, I2, J2, K1. In addition, phylogenetic relationships of the recovered populations were analysed using sequences of the near full length small subunit (SSU) and D2-D3 segments of large subunit (LSU) rRNA genes. [ABSTRACT FROM AUTHOR]

Published
2024
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42. Making Urban Commons

Author

Yang, Yimeng

Abstract

The urban commons is a public resource that citizens collectively manage and enjoy, but it is also a collective political experience beyond the state and the market (Huron, 2017). Thus, the urban commons is not just a thing, but a particular social relation and the struggle towards the urban commons is also an ongoing social practice that makes alternative relations (Harvey, 2012; Caffentzis and Federici, 2013; Tan, 2018). It is worth noting that the digital commons are emerging with the development of Internet technologies (Stalder, 2010). People in the digital world can access data, information, and knowledge at a lower cost and are more likely to produce based on the motivation of communication and sharing rather than on profit and exchange (Benkler, 2008)., UXUC - User Experience and Urban Creativity, Vol 4 No 1 (2022): Art, Urban Commons and Social Change

Published
2022
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43. An Adaptive Resource Control Mechanism in Multi-hop Ad-Hoc Networks

Author

Yang, Yimeng, Heijenk, Geert, Haverkort, Boudewijn R., Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Nierstrasz, Oscar, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Sudan, Madhu, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Vardi, Moshe Y., Series editor, Weikum, Gerhard, Series editor, Masip-Bruin, Xavier, editor, Verchere, Dominique, editor, Tsaoussidis, Vassilis, editor, and Yannuzzi, Marcelo, editor

Published
2011
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44. Investigation for the movement of the laser entrance hole and bubble plasmas in laser-driven hohlraum

Author

Li, Qi, primary, Guo, Liang, additional, Li, Sanwei, additional, Li, Zhichao, additional, Deng, Bo, additional, Wang, Qiangqiang, additional, Deng, Keli, additional, Cao, Zhurong, additional, Du, Huabin, additional, Che, Xinshen, additional, Yang, Yimeng, additional, Hou, Lifei, additional, Gong, Tao, additional, Yang, Dong, additional, and Yang, Jiamin, additional

Published
2022
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45. Characterization of radiation drive by measuring the localized re-emitted flux from the capsule in inertial confinement fusion experiments

Author

Xie, Xufei, primary, Wu, Changshu, additional, Chen, Jinwen, additional, Liu, Shenye, additional, Hou, Lifei, additional, Du, Huabin, additional, Cai, Hongbo, additional, Guo, Liang, additional, Ren, Kuan, additional, Li, Zhichao, additional, Yang, Dong, additional, Li, Sanwei, additional, Ge, Fengjun, additional, Li, Xin, additional, Huang, Yunbao, additional, Jing, Longfei, additional, Shang, Wanli, additional, Liu, Yaoyuan, additional, Jiang, Xiaohua, additional, Zhan, Xiayu, additional, Yang, Yimeng, additional, Wang, Feng, additional, He, Haien, additional, Zou, Shiyang, additional, Yang, Jiamin, additional, Jiang, Shaoen, additional, Zhang, Baohan, additional, and Ding, Yongkun, additional

Published
2022
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