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A Review of Sieve Algorithms in Solving the Shortest Lattice Vector Problem

Zedong Sun, Zedong Sun, Chunxiang Gu, Chunxiang Gu, Yonghui Zheng, Yonghui Zheng
2020 IEEE Access  
doi:10.1109/access.2020.3031276 fatcat:6mq4w466obh2zbw4bbgutqqm4m

H3K36 trimethylation-mediated biological functions in cancer

Chu Xiao, Tao Fan, He Tian, Yujia Zheng, Zheng Zhou, Shuofeng Li, Chunxiang Li, Jie He
2021 Clinical Epigenetics  
AbstractHistone modification is an important form of epigenetic regulation. Thereinto, histone methylation is a critical determination of chromatin states, participating in multiple cellular processes. As a conserved histone methylation mark, histone 3 lysine 36 trimethylation (H3K36me3) can mediate multiple transcriptional-related events, such as the regulation of transcriptional activity, transcription elongation, pre-mRNA alternative splicing, and RNA m6A methylation. Additionally, H3K36me3
more » ... lso contributes to DNA damage repair. Given the crucial function of H3K36me3 in genome regulation, the roles of H3K36me3 and its sole methyltransferase SETD2 in pathogenesis, especially malignancies, have been emphasized in many studies, and it is conceivable that disruption of histone methylation regulatory network composed of "writer", "eraser", "reader", and the mutation of H3K36me3 codes have the capacity of powerfully modulating cancer initiation and development. Here we review H3K36me3-mediated biological processes and summarize the latest findings regarding its role in cancers. We highlight the significance of epigenetic combination therapies in cancers.
doi:10.1186/s13148-021-01187-2 pmid:34715919 pmcid:PMC8555273 fatcat:ehdiuctudjdqtcl6eunukngmeq

GADD45B as a Prognostic and Predictive Biomarker in Stage II Colorectal Cancer

Zhixun Zhao, Yibo Gao, Xu Guan, Zheng Liu, Zheng Jiang, Xiuyun Liu, Huixin Lin, Ming Yang, Chunxiang Li, Runkun Yang, Shuangmei Zou, Xishan Wang
2018 Genes  
GADD45B acts as a member of the growth arrest DNA damage-inducible gene family, which has demonstrated to play critical roles in DNA damage repair, cell growth, and apoptosis. This study aimed to explore the potential relationship between GADD45B expression and tumor progression and evaluate the clinical value of GADD45B in stage II colorectal cancer (CRC). The expression patterns and prognostic value of GADD45B in CRC were analyzed based on The Cancer Genomic Atlas (TCGA). GADD45B expression
more » ... atures of 306 patients with stage II CRC and 201 patients with liver metastasis of CRC were investigated using immunochemical staining on tissue microarrays. Afterward, survival analysis and stratification analysis were performed in stage II to explore the prognostic and predictive significance of GADD45B. Overexpressed GADD45B is associated with poorer prognosis for CRC patients both in overall survival (OS) (p < 0.001) and disease-free survival (DFS) (p = 0.001) based on the TCGA database. Analysis results according to the stage II CRC cohort and the liver metastatic CRC cohort revealed that GADD45B was gradually upregulated in normal mucosa including primary colorectal cancer (PCC). Colorectal liver metastases (CLM) tissues were arranged in order (normal tissue vs. PCC p = 0.005 and PCC vs. CLM p = 0.001). The low GADD45B group had a significantly longer five-year OS (p = 0.001) and progression-free survival (PFS) (p < 0.001) than the high GADD45B group for the stage II patients. The multivariate Cox regression analysis results proved that the expression level of GADD45B was an independent prognostic factor for stage II after radical surgery (OS: Hazard Ratio (HR) 0.479, [95% confidence interval (CI) 0.305–0.753] and PFS:HR 0.490, [95% CI 0.336–0.714]). In high GADD45B expression subgroup of stage II cohort, the patients who underwent adjuvant chemotherapy had longer PFS than those who did not (p = 0.008). High expression levels of GADD45B is an independent prognostic factor of decreased OS and PFS in stage II CRC patients. The stage II CRC patients with high GADD45B expression might benefit from adjuvant chemotherapy.
doi:10.3390/genes9070361 pmid:30029519 pmcid:PMC6071283 fatcat:xorpwchz4ndhri4yp25ngzntri

SDSS--IV MaNGA : The Inner Density Slopes of nearby galaxies [article]

Ran Li, Hongyu Li, Shi Shao, Shengdong Lu, Kai Zhu, Chunxiang Wang, Liang Gao, Shude Mao, Aaron A. Dutton, Junqiang Ge, Yunchong Wang, Alexie Leauthaud, Zheng Zheng (+2 others)
2019 arXiv   pre-print
We derive the mass weighted total density slopes within the effective (half-light) radius, γ', for more than 2000 nearby galaxies from the SDSS-IV MaNGA survey using Jeans-anisotropic-models applied to IFU observations. Our galaxies span a wide range of the stellar mass (10^9 M_< M_* < 10^12 M_) and the velocity dispersion (30 km/s < σ_v < 300 km/s). We find that for galaxies with velocity dispersion σ_v>100 km/s, the density slope has a mean value 〈γ^'〉 = 2.24 and a dispersion σ_γ=0.22, almost
more » ... independent of velocity dispersion. A clear turn over in the γ'-σ_v relation is present at σ∼ 100 km/s, below which the density slope decreases rapidly with σ_v. Our analysis shows that a large fraction of dwarf galaxies (below M_* = 10^10 M_) have total density slopes shallower than 1, which implies that they may reside in cold dark matter halos with shallow density slopes. We compare our results with that of galaxies in hydrodynamical simulations of EAGLE, Illustris and IllustrisTNG projects, and find all simulations predict shallower density slopes for massive galaxies with high σ_v. Finally, we explore the dependence of γ' on the positions of galaxies in halos, namely centrals vs. satellites, and find that for the same velocity dispersion, the amplitude of γ' is higher for satellite galaxies by about 0.1.
arXiv:1903.09282v1 fatcat:pnbhshlhibaltikhuvhmvj3u7y

Identification and characterization of ANO9 in stage II and III colorectal carcinoma

Chunxiang Li, Sanjun Cai, Xishan Wang, Zheng Jiang
2015 OncoTarget  
and Objectives: The precise role and potential underlying mechanisms of anoctamin 9 (ANO9) remain largely unknown. This study aims to characterize the role and oncogenic mechanisms of ANO9 in stage II and III colorectal cancer (CRC). Methods: We examined the expression of ANO9 in colorectal cancerous tissues and cells using real-time quantitative PCR and immunohistochemistry, respectively. Multiple cellular and molecular approaches such as gene transfection, CCK-8 assay, flow cytometry, and
more » ... sion assay were also performed to explore its oncogenic mechanisms. Furthermore, the clinical significance of ANO9 in clinical CRC specimens was assessed by clinical correlation and survival analyses. Results: Lower expression of ANO9 messenger RNA (mRNA) was frequently detected both in CRC tissues with recurrence and metastasis-derived cell lines. Compared with matched nontumorous tissues, lower expression of ANO9 protein was observed in tumors, which was significantly correlated with tumorigenesis (p < 0.05). In vitro functional studies showed that ANO9 contributed to tumor cell proliferation, apoptosis, and invasion. Moreover, investigation of clinical CRC specimens showed that ANO9 were markedly overexpressed in metastatic tissue compared with primary tissue. Decreased expression of ANO9 was correlated with poor prognostic outcomes. Conclusions: This study highlighted the role of ANO9 in progression and metastasis of stage II and III CRC. These findings suggested that up-regulation of ANO9, as a metastasis-related gene, could be a novel approach for inhibiting CRC progression.
doi:10.18632/oncotarget.4979 pmid:26317553 pmcid:PMC4745729 fatcat:wpg2s7itsjfmfkt47ha54gf5ei

Nicotianamine, a Novel Enhancer of Rice Iron Bioavailability to Humans

Luqing Zheng, Zhiqiang Cheng, Chunxiang Ai, Xinhang Jiang, Xiaoshu Bei, Ye Zheng, Raymond P. Glahn, Ross M. Welch, Dennis D. Miller, Xin Gen Lei, Huixia Shou, Edward Newbigin
2010 PLoS ONE  
Polished rice is a staple food for over 50% of the world's population, but contains little bioavailable iron (Fe) to meet human needs. Thus, biofortifying the rice grain with novel promoters or enhancers of Fe utilization would be one of the most effective strategies to prevent the high prevalence of Fe deficiency and iron deficiency anemia in the developing world. Methodology/Principal Findings: We transformed an elite rice line cultivated in Southern China with the rice nicotianamine synthase
more » ... gene (OsNAS1) fused to a rice glutelin promoter. Endosperm overexpression of OsNAS1 resulted in a significant increase in nicotianamine (NA) concentrations in both unpolished and polished grain. Bioavailability of Fe from the high NA grain, as measured by ferritin synthesis in an in vitro Caco-2 cell model that simulates the human digestive system, was twice as much as that of the control line. When added at 1:1 molar ratio to ferrous Fe in the cell system, NA was twice as effective when compared to ascorbic acid (one of the most potent known enhancers of Fe bioavailability) in promoting more ferritin synthesis. Conclusions: Our data demonstrated that NA is a novel and effective promoter of iron utilization. Biofortifying polished rice with this compound has great potential in combating global human iron deficiency in people dependent on rice for their sustenance.
doi:10.1371/journal.pone.0010190 pmid:20419136 pmcid:PMC2855712 fatcat:7647aqetlvbircsfndwxj525ry

LncRNA EGOT/miR-211-5p Affected Radiosensitivity of Rectal Cancer by Competitively Regulating ErbB4

Chunxiang Li, Hengchang Liu, Ran Wei, Zheng Liu, Haipeng Chen, Xu Guan, Zhixun Zhao, Xishan Wang, Zheng Jiang
2021 OncoTargets and Therapy  
Long non-coding ribonucleic acids (lncRNAs) are involved in the progression of cancers and affect the response to radiation therapy. This study was to investigate the mechanism of lncRNA EGOT in the radiosensitivity of rectal cancer. The mRNA expression of EGOT, miR-211-5p and ErbB4 in rectal cancer tissues and cells was detected by qRT-PCR. The protein expression of ErbB4 was detected by Western blot. Dual-luciferase reporter assay and ribonucleic acid immunoprecipitation (RIP) were used to
more » ... firm the interaction between EGOT and miR-211-5p or miR-211-5p and ErbB4. Transfection technology was used to down-regulate and up-regulate the expression of EGOT and miR-211-5p in rectal cancer cells, respectively. MTT, colony formation and flow cytometry were used to detect the effect of EGOT and miR-211-5p on proliferation, invasion, migration and apoptosis of rectal cancer cells. The expression of EGOT was up-regulated in rectal cancer tissues and cells, and the expression of EGOT was related to the late stage of pathology. EGOT knockdown inhibited the proliferation and colony formation of rectal cancer cells and induced the apoptosis of rectal cancer cells. Moreover, EGOT knockdown was significantly enhanced the effects of radiotherapy on rectal cancer in vivo and in vitro. Furthermore, EGOT was found to serve as a sponge of miR-211-5p, and ErbB4 was a downstream target of miR-211-5p. EGOT enhanced the expression of ErbB4 by regulating miR-211-5p. MiR-211-5p inhibitor restored the effect of EGOT knockdown on the radiosensitivity of rectal cancer. Down-regulation of EGOT could inhibit the growth of rectal cancer cells by regulating the miR-211-5p/ErbB4 axis and improve the radiosensitivity of rectal cancer cells. EGOT may be a new therapeutic target for rectal cancer.
doi:10.2147/ott.s256989 pmid:33953571 pmcid:PMC8091867 fatcat:2jauzifd6rgqdcge2luomm5nqe

Integrating cross-linking experiments with ab initio protein-protein docking [article]

Thom Vreven, Devin K Schweppe, Juan D Chavez, Chad R Weisbrod, Sayaka Shibata, Chunxiang Zheng, James E Bruce, Zhiping Weng
2018 bioRxiv   pre-print
Ab initio protein-protein docking algorithms often rely on experimental data to identify the most likely complex structure. We integrated protein-protein docking with the experimental data of chemical cross-linking followed by mass spectrometry. We tested our approach using 12 cases that resulted from an exhaustive search of the Protein Data Bank for protein complexes with cross-links identified in our experiments. We implemented cross-links as constraints based on Euclidean distance or
more » ... ume distance. For most test cases the rank of the top-scoring near-native prediction was improved by at least two fold compared with docking without the cross-link information, and the success rates for the top 5 and top 10 predictions doubled. Our results demonstrate the delicate balance between retaining correct predictions and eliminating false positives. Several test cases had multiple components with distinct interfaces, and we present an approach for assigning cross-links to the interfaces. Employing the symmetry information for these cases further improved the performance of complex structure prediction.
doi:10.1101/275891 fatcat:giwt7ixvefdxngfqyhvvvpww3e

An Integrated Approach to Uncover Driver Genes in Breast Cancer Methylation Genomes

Xiaopei Shen, Shan Li, Lin Zhang, Hongdong Li, Guini Hong, XianXiao Zhou, Tingting Zheng, Wenjing Zhang, Chunxiang Hao, Tongwei Shi, Chunyang Liu, Zheng Guo (+1 others)
2013 PLoS ONE  
Cancer cells typically exhibit large-scale aberrant methylation of gene promoters. Some of the genes with promoter methylation alterations play "driver" roles in tumorigenesis, whereas others are only "passengers". Results: Based on the assumption that promoter methylation alteration of a driver gene may lead to expression alternation of a set of genes associated with cancer pathways, we developed a computational framework for integrating promoter methylation and gene expression data to
more » ... driver methylation aberrations of cancer. Applying this approach to breast cancer data, we identified many novel cancer driver genes and found that some of the identified driver genes were subtypespecific for basal-like, luminal-A and HER2+ subtypes of breast cancer. Conclusion: The proposed framework proved effective in identifying cancer driver genes from genome-wide gene methylation and expression data of cancer. These results may provide new molecular targets for potential targeted and selective epigenetic therapy.
doi:10.1371/journal.pone.0061214 pmid:23579546 pmcid:PMC3620319 fatcat:welnxero65fh5itbsx23oiy6uu

Cross-linking Measurements ofIn VivoProtein Complex Topologies

Chunxiang Zheng, Li Yang, Michael R. Hoopmann, Jimmy K. Eng, Xiaoting Tang, Chad R. Weisbrod, James E. Bruce
2011 Molecular & Cellular Proteomics  
Identification and measurement of in vivo protein interactions pose critical challenges in the goal to understand biological systems. The measurement of structures and topologies of proteins and protein complexes as they exist in cells is particularly challenging, yet critically important to improve understanding of biological function because proteins exert their intended function only through the structures and interactions they exhibit in vivo. In the present study, protein interactions in
more » ... coli cells were identified in our unbiased cross-linking approach, yielding the first in vivo topological data on many interactions and the largest set of identified in vivo crosslinked peptides produced to date. These data show excellent agreement with protein and complex crystal structures where available. Furthermore, our unbiased data provide novel in vivo topological information that can impact understanding of biological function, even for cases where high resolution structures are not yet available. Molecular & Cellular 1 The abbreviations used are: PIR, protein interaction reporter; Omp A, outer membrane protein A; LC-MS/MS, liquid chromatography tandem MS; LTQ-FT MS, linear trap quadrupole-Fourier transform MS; ISCID, in-source collision-induced dissociation; PDB, Protein Data Bank. Research
doi:10.1074/mcp.m110.006841 pmid:21697552 pmcid:PMC3205858 fatcat:5p66tg6ncjg5bkvzkfcw4um7hq

Quantitative interactome analysis reveals a chemoresistant edgotype

Juan D. Chavez, Devin K. Schweppe, Jimmy K. Eng, Chunxiang Zheng, Alex Taipale, Yiyi Zhang, Kohji Takara, James E. Bruce
2015 Nature Communications  
Chemoresistance is a common mode of therapy failure for many cancers. Tumours develop resistance to chemotherapeutics through a variety of mechanisms, with proteins serving pivotal roles. Changes in protein conformations and interactions affect the cellular response to environmental conditions contributing to the development of new phenotypes. The ability to understand how protein interaction networks adapt to yield new function or alter phenotype is limited by the inability to determine
more » ... ral and protein interaction changes on a proteomic scale. Here, chemical crosslinking and mass spectrometry were employed to quantify changes in protein structures and interactions in multidrug-resistant human carcinoma cells. Quantitative analysis of the largest crosslinking-derived, protein interaction network comprising 1,391 crosslinked peptides allows for 'edgotype' analysis in a cell model of chemoresistance. We detect consistent changes to protein interactions and structures, including those involving cytokeratins, topoisomerase-2-alpha, and post-translationally modified histones, which correlate with a chemoresistant phenotype.
doi:10.1038/ncomms8928 pmid:26235782 pmcid:PMC4532879 fatcat:7nccejnhfrdxzgedsw6b2fdqbi

Motor Dynamic Loading and Comprehensive Test System Based on FPGA and MCU

Chunxiang Zhu, Linxin Bao, Bowen Zheng, Jiacheng Qian, Yongdong Cai, Binrui Wang
2022 Electronics  
In view of the problem that the traditional motor test system cannot directly test the transient parameters of the motor and the dynamic arbitrary load loading requirements during motor loading, as well as the high cost of implementation, this research uses STM32+FPGA as the core to form the main control of the motor test system unit, combining the superior control performance of the ARM processor and the high-speed data processing advantages of FPGA. FPGA and STM32 are controlled by the FSMC
more » ... s communication and data ping-pong algorithm. Using this method, a small-size control core board in the motor test system is manufactured. It can be embedded in the existing traditional dynamometer system to improve the dynamometer transient parameter test and the dynamic motor loading performance. The experimental results show that the system can basically meet the requirements of the motor transient test and dynamic loading, and can achieve the fastest data refresh rate of 1 ms when measuring the motor's speed and torque, as well as arbitrary waveform loading within a 100 M sampling frequency, with a loading error of 0.8%. It satisfies the motor transient test and dynamic loading requirements.
doi:10.3390/electronics11091317 fatcat:iocnayklmngm5hd6ly6rbjc5aa

Apolipoprotein E Overexpression Is Associated With Tumor Progression and Poor Survival in Colorectal Cancer

Zhixun Zhao, Shuangmei Zou, Xu Guan, Meng Wang, Zheng Jiang, Zheng Liu, Chunxiang Li, Huixin Lin, Xiuyun Liu, Runkun Yang, Yibo Gao, Xishan Wang
2018 Frontiers in Genetics  
., 2005; Zheng et al., 2018) .  ... 
doi:10.3389/fgene.2018.00650 pmid:30631342 pmcid:PMC6315167 fatcat:mya5a72mynd3pp4hu5j5c2i4da

ERAP2 Is Associated With Immune Infiltration and Predicts Favorable Prognosis in SqCLC

Zhenlin Yang, He Tian, Fenglong Bie, Jiachen Xu, Zheng Zhou, Junhui Yang, Renda Li, Yue Peng, Guangyu Bai, Yanhua Tian, Ying Chen, Lei Liu (+8 others)
2021 Frontiers in Immunology  
, Zheng, Wang, Li, Gao and He.  ...  Y, Zheng B, Wang J, Li C, Gao S and He J (2021) ERAP2 Is Associated With Immune Infiltration and Predicts Favorable Prognosis in SqCLC.  ... 
doi:10.3389/fimmu.2021.788985 pmid:34992605 pmcid:PMC8725995 fatcat:dn3njfdrszfbrcfj5ppcvcgila

Analysis of Spatiotemporal Characteristics of Pandemic SARS Spread in Mainland China

Chunxiang Cao, Wei Chen, Sheng Zheng, Jian Zhao, Jinfeng Wang, Wuchun Cao
2016 BioMed Research International  
Authors' Contributions Chunxiang Cao and Wei Chen were the main researchers and responsible for the data analysis and paper writing.  ...  Wei Chen and Sheng Zheng performed data processing and model implementation. Jinfeng Wang commented on idea selection. Wuchun Cao provided SARS data and supervised the modelling details.  ... 
doi:10.1155/2016/7247983 pmid:27597972 pmcid:PMC5002496 fatcat:ycydlzc6qfcdjaxqic7teloj3e
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