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6,370 results on '"Chen, YuanYuan"'

165. A hydrophilic microenvironment in the substrate-translocating groove of the YidC membrane insertase is essential for enzyme function

Author

Chen, Yuanyuan, Sotomayor, Marcos, Capponi, Sara, Hariharan, Balasubramani, Sahu, Indra D, Haase, Maximilian, Lorigan, Gary A, Kuhn, Andreas, White, Stephen H, and Dalbey, Ross E

Subjects
Biochemistry and Cell Biology, Biological Sciences, Infectious Diseases, Bacillus subtilis, Cell Membrane, Escherichia coli, Escherichia coli Proteins, Hydrophobic and Hydrophilic Interactions, Membrane Transport Proteins, Structure-Activity Relationship, S. mutans, YidC, membrane biogenesis, membrane transport, molecular dynamics, Chemical Sciences, Medical and Health Sciences, Biochemistry & Molecular Biology, Biological sciences, Biomedical and clinical sciences, Chemical sciences
Abstract

The YidC family of proteins are membrane insertases that catalyze the translocation of the periplasmic domain of membrane proteins via a hydrophilic groove located within the inner leaflet of the membrane. All homologs have a strictly conserved, positively charged residue in the center of this groove. In Bacillus subtilis, the positively charged residue has been proposed to be essential for interacting with negatively charged residues of the substrate, supporting a hypothesis that YidC catalyzes insertion via an early-step electrostatic attraction mechanism. Here, we provide data suggesting that the positively charged residue is important not for its charge but for increasing the hydrophilicity of the groove. We found that the positively charged residue is dispensable for Escherichia coli YidC function when an adjacent residue at position 517 was hydrophilic or aromatic, but was essential when the adjacent residue was apolar. Additionally, solvent accessibility studies support the idea that the conserved positively charged residue functions to keep the top and middle of the groove sufficiently hydrated. Moreover, we demonstrate that both the E. coli and Streptococcus mutans YidC homologs are functional when the strictly conserved arginine is replaced with a negatively charged residue, provided proper stabilization from neighboring residues. These combined results show that the positively charged residue functions to maintain a hydrophilic microenvironment in the groove necessary for the insertase activity, rather than to form electrostatic interactions with the substrates.

Published
2022

166. Non-principal axis rotation in binary asteroid systems and how it weakens the BYORP effect

Author

Quillen, Alice C., LaBarca, Anthony, and Chen, YuanYuan

Subjects
Astrophysics - Earth and Planetary Astrophysics
Abstract

Using viscoelastic mass/spring model simulations, we explore tidal evolution and migration of compact binary asteroid systems. We find that after the secondary is captured into a spin-synchronous state, non-principal axis rotation in the secondary can be long-lived. The secondary's long axis can remain approximately aligned along the vector connecting secondary to primary while the secondary rocks back and forth about its long axis. Inward orbital semi-major axis migration can also resonantly excite non-principal axis rotation. By estimating solar radiation forces on triangular surface meshes, we show that the magnitude of the BYORP effect induced torque is sensitive to the secondary's spin state. Non-principal axis rotation within the 1:1 spin-orbit resonance can reduce the BYORP torque or cause frequent reversals in its direction., Comment: to be published in Icarus

Published
2021
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167. Temporal dissipative structures in optical Kerr resonators with transient loss fluctuation

Author

Chen, Yuanyuan, Liu, Tuo, Sun, Suwan, and Guo, Hairun

Subjects
Physics - Optics
Abstract

Dissipative structures are the result of spontaneous symmetry breaking in a dynamic open system, which is induced by either the nonlinear effect or loss fluctuations. While optical temporal dissipative solitons in nonlinear Kerr cavities has been widely studied, they are operated in a red-detuned regime that is non-trivial to access. Here, we demonstrate an emergent dissipative soliton state in optical cavities in the presence of loss fluctuations, which is accessible by self-evolution of the system and is operated in resonance. We numerically investigate both the effect of loss modulation and the effect of saturable absorption, based on a standard dissipative and Kerr-nonlinear microresonator model, and observe stable soliton states in a close-to-zero detuning region. The self-starting soliton state working in resonance is potentially of wide interest, which would not only ease the operation for ultrafast temporal soliton generation, but also imply a high conversion efficiency for soliton micro-combs.

Published
2021
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168. FocusNetv2: Imbalanced Large and Small Organ Segmentation with Adversarial Shape Constraint for Head and Neck CT Images

Author

Gao, Yunhe, Huang, Rui, Yang, Yiwei, Zhang, Jie, Shao, Kainan, Tao, Changjuan, Chen, Yuanyuan, Metaxas, Dimitris N., Li, Hongsheng, and Chen, Ming

Subjects
Electrical Engineering and Systems Science - Image and Video Processing, Computer Science - Computer Vision and Pattern Recognition
Abstract

Radiotherapy is a treatment where radiation is used to eliminate cancer cells. The delineation of organs-at-risk (OARs) is a vital step in radiotherapy treatment planning to avoid damage to healthy organs. For nasopharyngeal cancer, more than 20 OARs are needed to be precisely segmented in advance. The challenge of this task lies in complex anatomical structure, low-contrast organ contours, and the extremely imbalanced size between large and small organs. Common segmentation methods that treat them equally would generally lead to inaccurate small-organ labeling. We propose a novel two-stage deep neural network, FocusNetv2, to solve this challenging problem by automatically locating, ROI-pooling, and segmenting small organs with specifically designed small-organ localization and segmentation sub-networks while maintaining the accuracy of large organ segmentation. In addition to our original FocusNet, we employ a novel adversarial shape constraint on small organs to ensure the consistency between estimated small-organ shapes and organ shape prior knowledge. Our proposed framework is extensively tested on both self-collected dataset of 1,164 CT scans and the MICCAI Head and Neck Auto Segmentation Challenge 2015 dataset, which shows superior performance compared with state-of-the-art head and neck OAR segmentation methods., Comment: Accepted by Medical Image Analysis

Published
2021
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184. Hippocampal circAnk3 Deficiency Causes Anxiety-like Behaviors and Social Deficits by Regulating the miR-7080-3p/IQGAP1 Pathway in Mice

Author

He, Yuman, Jiang, Linhong, Liu, Haxiaoyu, Bu, Qian, Kuang, Weihong, Zhao, Ying, Chen, Yaxing, Zhang, Ni, Xiao, Yuzhou, Li, Shu, Chen, Rong, Han, Shuang, Zhou, Yuanyi, Zhang, Jiamei, Wan, Xuemei, Xu, Rui, Wang, Shaomin, Zhang, Haoluo, Gu, Hui, Wei, Qingfan, Qin, Feng, Zhao, Yue, Li, Hongchun, Wang, Liang, Wang, Xiaojie, Wang, Yonghai, Dai, Yanping, Li, Min, Chen, Yuanyuan, Wang, Hongbo, Tian, Jingwei, Zhao, Yinglan, and Cen, Xiaobo

Published
2024
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