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1,429 results on '"Wang Shengjie"'

151. LncRNA CCRR maintains Ca2+ homeostasis against myocardial infarction through the FTO-SERCA2a pathway.

Author

Yang, Hua, Xuan, Lina, Wang, Shengjie, Luo, Huishan, Duan, Xiaomeng, Guo, Jianjun, Cui, Shijia, Xin, Jieru, Hao, Junwei, Li, Xiufang, Chen, Jun, Sun, Feihan, Hu, Xiaolin, Li, Siyun, Zhang, Ying, Jiao, Lei, Yang, Baofeng, and Sun, Lihua

Abstract

Cardiac conduction regulatory RNA (CCRR) has been documented as an antiarrhythmic lncRNA in our earlier investigation. This study aimed to evaluate the effects of CCRR on SERCA2a and the associated Ca2+ homeostasis in myocardial infarction (MI). Overexpression of CCRR via AAV9-mediated delivery not only partially reversed ischemia-induced contractile dysfunction but also alleviated abnormal Ca2+ homeostasis and reduced the heightened methylation level of SERCA2a following MI. These effects were also observed in CCRR over-expressing transgenic mice. A conserved sequence domain of CCRR mimicked the protective function observed with the full length. Furthermore, silencing CCRR in healthy mice led to intracellular Ca2+ overloading of cardiomyocytes. CCRR increased SERCA2a protein stability by upregulating FTO expression. The direct interaction between CCRR and FTO protein was characterized by RNA-binding protein immunoprecipitation (RIP) analysis and RNA pulldown experiments. Activation of NFATc3 was identified as an upstream mechanism responsible for CCRR downregulation in MI. This study demonstrates that CCRR is a protective lncRNA that acts by maintaining the function of FTO, thereby reducing the m6A RNA methylation level of SERCA2a, ultimately preserving calcium homeostasis for myocardial contractile function in MI. Therefore, CCRR may be considered a promising therapeutic strategy with a beneficial role in cardiac pathology. [ABSTRACT FROM AUTHOR]

Published
2024
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167. Faster graphical model identification of tandem mass spectra using peptide word lattices

Author

Wang, Shengjie, Halloran, John T., Bilmes, Jeff A., and Noble, William S.

Subjects
Quantitative Biology - Molecular Networks, Statistics - Machine Learning
Abstract

Liquid chromatography coupled with tandem mass spectrometry, also known as shotgun proteomics, is a widely-used high-throughput technology for identifying proteins in complex biological samples. Analysis of the tens of thousands of fragmentation spectra produced by a typical shotgun proteomics experiment begins by assigning to each observed spectrum the peptide hypothesized to be responsible for generating the spectrum, typically done by searching each spectrum against a database of peptides. We have recently described a machine learning method---Dynamic Bayesian Network for Rapid Identification of Peptides (DRIP)---that not only achieves state-of-the-art spectrum identification performance on a variety of datasets but also provides a trainable model capable of returning valuable auxiliary information regarding specific peptide-spectrum matches. In this work, we present two significant improvements to DRIP. First, we describe how to use word lattices, which are widely used in natural language processing, to significantly speed up DRIP's computations. To our knowledge, all existing shotgun proteomics search engines compute independent scores between a given observed spectrum and each possible candidate peptide from the database. The key idea of the word lattice is to represent the set of candidate peptides in a single data structure, thereby allowing sharing of redundant computations among the different candidates. We demonstrate that using lattices in conjunction with DRIP leads to speedups on the order of tens across yeast and worm data sets. Second, we introduce a variant of DRIP that uses a discriminative training framework, performing maximum mutual entropy estimation rather than maximum likelihood estimation. This modification improves DRIP's statistical power, enabling us to increase the number of identified spectrum at a 1% false discovery rate on yeast and worm data sets.

Published
2014

177. Multiple Location Profiling for Users and Relationships from Social Network and Content

Author

Li, Rui, Wang, Shengjie, and Chang, Kevin Chen-Chuan

Subjects
Computer Science - Databases
Abstract

Users' locations are important for many applications such as personalized search and localized content delivery. In this paper, we study the problem of profiling Twitter users' locations with their following network and tweets. We propose a multiple location profiling model (MLP), which has three key features: 1) it formally models how likely a user follows another user given their locations and how likely a user tweets a venue given his location, 2) it fundamentally captures that a user has multiple locations and his following relationships and tweeted venues can be related to any of his locations, and some of them are even noisy, and 3) it novelly utilizes the home locations of some users as partial supervision. As a result, MLP not only discovers users' locations accurately and completely, but also "explains" each following relationship by revealing users' true locations in the relationship. Experiments on a large-scale data set demonstrate those advantages. Particularly, 1) for predicting users' home locations, MLP successfully places 62% users and outperforms two state-of-the-art methods by 10% in accuracy, 2) for discovering users' multiple locations, MLP improves the baseline methods by 14% in recall, and 3) for explaining following relationships, MLP achieves 57% accuracy., Comment: VLDB2012

Published
2012

183. Spatial distribution characteristics of stable hydrogen and oxygen isotopes in surface waters on the northern slope of the Kunlun Mountains.

Author

SHI Yudong, WANG Shengjie, ZHANG Mingjun, ZHU Chenggang, and CHE Yanjun

Subjects
OXYGEN isotopes, HYDROGEN isotopes, STABLE isotopes, WESTERLIES, SCIENTIFIC expeditions
Abstract

Stable hydrogen and oxygen isotopes are widely used as tracers in studying hydrologic processes. Surface water is an important component of the water cycle, and it is an effective vehicle for analyzing regional moisture sources and modern hydrologic processes. We collected surface water samples from August 2018 to August 2023 on the northern slope of the Kunlun Mountains during the Third Xinjiang Scientific Expedition and measured the stable hydrogen and oxygen isotope values. Additionally, we compiled the previous surface water isotope data in the region. We analyzed the spatial distribution characteristics of the stable hydrogen and oxygen isotopes of surface water on the northern slope of the Kunlun Mountains. The results showed that: (1) The surface water isotope values on the northern slope of the Kunlun Mountains showed spatial variations characterized by low values in the west and high values in the east. The local surface water line is δ² H=5.98xδ18 O-6.86 (R²=0.65, n=141). (2) A comparison of the stable isotope values of surface water and precipitation on the northern slope of the Kunlun Mountains reveals that the regional surface water isotope value averages are generally lower than the weighted precipitation isotope values. (3) The spatial distribution of surface water isotopes on the northern slope of the Kunlun Mountains is influenced by the interplay of two key factors: the water vapor advection by westerly winds and the local recycled moisture; additionally, evaporation also changed the regional surface water isotope values. [ABSTRACT FROM AUTHOR]

Published
2024
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185. Inhibition of circ_0000231 suppresses oxidized low density lipoprotein-induced apoptosis, autophagy and inflammation in human umbilical vein endothelial cells by regulating miR-590-5p/PDCD4 axis.

Author

Lin, Haiyan, Gao, Da, Wang, Shengjie, Wang, Zicheng, Guan, Haiwang, Wang, Yanwei, and Zhou, Ying

Subjects
ENZYME-linked immunosorbent assay, APOPTOSIS, CIRCULAR RNA, UMBILICAL veins, ENDOTHELIAL cells
Abstract

BACKGROUND: Circular RNAs (circRNAs) are the emerging informative RNAs, involved in cardiovascular diseases including atherosclerosis (AS). Endothelial injury is the initial qualitative change of AS. Thus, the objective of this study was to confirm the dysregulation and mechanism of circ_0000231 in cell model of AS at early stage in human umbilical vein endothelial cells (HUVECs) induced by oxidized low-density lipoprotein (ox-LDL). METHODS: The expression of circ_0000231, miR-590-5p and programmed cell death 4 (PDCD4) was detected using real-time quantitative PCR and western blot. Cell injury was measured with MTT, flow cytometry, caspase-3 activity assay and enzyme-linked immunosorbent assay (ELISA). The interaction among circ_0000231, miR-590-5p and PDCD4 was validated by dual-luciferase reporter assay, RNA immunoprecipitation (RIP) and pull-down assays. RESULTS: Stress ox-LDL decreased cell viability, and increased apoptosis rate and caspase-3 activity in HUVECs in a dose- and time-dependent manner in concomitant with promotions of interleukin-6, interleukin-1β, tumor necrosis factor-α, LC3-II/I and Beclin-1 levels. Besides, circ_0000231 and PDCD4 expressions were upregulated, and miR-590-5p was downregulated in ox-LDL-stimulated HUVECs. Functionally, knockdown of circ_0000231 and overexpression of miR-590-5p could suppress ox-LDL-elicited above effects on apoptosis, autophagy and inflammatory response, accompanied with PDCD4 downregulation. Physically, miR-590-5p could directly interact with circ_0000231 and PDCD4. CONCLUSION: Downregulation of circ_0000231 suppresses HUVECs from ox-LDL-induced injury partially through regulating miR-590-5p/PDCD4 axis via competing endogenous RNA mechanism, showing a novel potential target for the pathology and treatment of endothelial injury in AS. [ABSTRACT FROM AUTHOR]

Published
2024
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