Browsing by Author "Huang, Yufei"

Now showing 1 - 5 of 5
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    Advancing Systems Biology in the International Conference on Intelligent Biology and Medicine (ICIBM) 2015
    (BioMed Central, 2016-08-26) Zhao, Zhongming; Liu, Yunlong; Huang, Yufei; Huang, Kun; Ruan, Jianhua; Department of Medical and Molecular Genetics, IU School of Medicine
    The 2015 International Conference on Intelligent Biology and Medicine (ICIBM 2015) was held on November 13-15, 2015 in Indianapolis, Indiana, USA. ICIBM 2015 included eight scientific sessions, three tutorial sessions, one poster session, and four keynote presentations that covered the frontier research in broad areas related to bioinformatics, systems biology, big data science, biomedical informatics, pharmacogenomics, and intelligent computing. Here, we present a summary of the 10 research articles that were selected from ICIBM 2015 and included in the supplement to BMC Systems Biology.
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    Coupling Coordination Relationship between Urban Sprawl and Urbanization Quality in the West Taiwan Strait Urban Agglomeration, China: Observation and Analysis from DMSP/OLS Nighttime Light Imagery and Panel Data
    (MDPI, 2020-10) Lu, Chunyan; Li, Lin; Lei, Yifan; Ren, Chunying; Su, Ying; Huang, Yufei; Chen, Yu; Lei, Shaohua; Fu, Weiwei; Earth Sciences, School of Science
    Urban sprawl is the most prominent characteristic of urbanization, and increasingly affects local and regional sustainable development. The observation and analysis of urban sprawl dynamics and their relationship with urbanization quality are essential for framing integrative urban planning. In this study, the urban areas of the West Taiwan Strait Urban Agglomeration (WTSUA) were extracted using nighttime light imagery from 1992 to 2013. The spatio-temporal characteristics and pattern of urban sprawl were quantitatively analyzed by combining an urban expansion rate index and a standard deviation ellipse model. The urbanization quality was assessed using an entropy weight model, and its relationship with urban sprawl was calculated by a coupling coordination degree model. The results showed that the urban area in the WTSUA experienced a significant increase, i.e., 18,806.73 km2, during the period 1992–2013. The central cities grew by 11.08% and noncentral cities by 27.43%, with a general uneven city rank-size distribution. The urban sprawl showed a circular expansion pattern, accompanied by a gradual centroid migration of urban areas from the southeast coast to the central-western regions. The coupling coordination level between urban expansion and urbanization quality increased from serious incoordination in 1992 to basic coordination in 2013. Dual driving forces involving state-led policies and market-oriented land reform had a positive influence on the harmonious development of urban sprawl and urbanization quality of the WTSUA. This research offers an effective approach to monitor changes in urban sprawl and explore the coupling coordination relationship between urban sprawl and urbanization quality. The study provides important scientific references for the formulation of future policies and planning for sustainable development in urban agglomerations.
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    Intelligent biology and medicine in 2015: advancing interdisciplinary education, collaboration, and data science
    (BioMed Central, 2016-08-22) Huang, Kun; Liu, Yunlong; Huang, Yufei; Li, Lang; Cooper, Lee; Ruan, Jianhua; Zhao, Zhongming; Department of Medical and Molecular Genetics, IU School of Medicine
    We summarize the 2015 International Conference on Intelligent Biology and Medicine (ICIBM 2015) and the editorial report of the supplement to BMC Genomics. The supplement includes 20 research articles selected from the manuscripts submitted to ICIBM 2015. The conference was held on November 13-15, 2015 at Indianapolis, Indiana, USA. It included eight scientific sessions, three tutorials, four keynote presentations, three highlight talks, and a poster session that covered current research in bioinformatics, systems biology, computational biology, biotechnologies, and computational medicine.
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    Screening of an epigenetic compound library identifies BRD4 as a potential antiviral target for hepatitis B virus covalently closed circular DNA transcription
    (Elsevier, 2023) Yu, Xiaoyang; Long, Quanxin; Shen, Sheng; Liu, Zhentao; Chandran, Jithin; Zhang, Junjie; Ding, Hao; Zhang, Hu; Cai, Dawei; Kim, Elena S.; Huang, Yufei; Guo, Haitao; Microbiology and Immunology, School of Medicine
    HBV cccDNA is the persistent form of viral genome, which exists in host cell nucleus as an episomal minichromosome decorated with histone and non-histone proteins. cccDNA is the authentic viral transcription template and resistant to current antivirals. Growing evidence shows that the transcriptional activity of cccDNA minichromosome undergoes epigenetic regulations, suggesting a new perspective for anti-cccDNA drug development through targeting histone modifications. In this study, we screened an epigenetic compound library in the cccDNA reporter cell line HepBHAe82, which produces the HA-tagged HBeAg in a cccDNA-dependent manner. Among the obtained hits, a bromodomain-containing protein 4 (BRD4) inhibitor MS436 exhibited marked inhibition of cccDNA transcription in both HBV stable cell line HepAD38 and HepG2-NTCP or primary human hepatocyte infection system under noncytotoxic concentrations. Chromatin immunoprecipitation (ChIP) assay demonstrated that MS436 dramatically reduced the enrichment of H3K27ac, an activating histone modification pattern, on cccDNA minichromosome. RNAseq differential analysis showed that MS436 does not drastically change host transcriptome or induce any known anti-HBV factors/pathways, indicating a direct antiviral effect of MS436 on cccDNA minichromosome. Interestingly, the MS436-mediated inhibition of cccDNA transcription is accompanied by cccDNA destabilization in HBV infection and a recombinant cccDNA system, indicating that BRD4 activity may also play a role in cccDNA maintenance. Furthermore, depletion of BRD4 by siRNA knockdown or PROTAC degrader resulted in cccDNA inhibition in HBV-infected HepG2-NTCP cells, further validating BRD4 as an antiviral target. Taken together, our study has demonstrated the practicality of HepBHAe82-based anti-HBV drug screening system and provided a proof-of-concept for targeting HBV cccDNA with epigenetic compounds.
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    The national nature reserves in China: Are they effective in conserving mangroves?
    (Elsevier, 2022) Lu, Chunyan; Li, Lin; Wang, Zili; Su, Yanlin; Su, Yue; Huang, Yufei; Jia, Mingming; Mao, Dehua; Earth and Environmental Sciences, School of Science
    Mangroves are high-productive ecosystems and globally protected. Establishing nature reserves aimed at counteracting the negative effects of anthropogenic activities is one of the most pivotal approaches to conserve mangrove ecosystems. Evaluation of the conservation effectiveness for mangrove nature reserves is thus indispensable for making knowledge-based conservation policies and funding-decisions by government and managers. In this study, using composited Landsat images by the Google Earth Engine cloud platform and object-oriented deep learning classification method, the land cover maps of national mangrove nature reserves (NMNRs) in China were obtained from 1987 to 2019. The systematic evaluation of conservation effectiveness for each NMNR was conducted by landscape metrics and an entropy weight model. Combined with the dynamics in mangrove distribution, human interference intensity, and natural environment change, the driving force factors affecting the conservation effectiveness for NMNRs were investigated. The results show that the total mangrove area in all NMNRs increased 968.6 ha during the study period, a 21.8 % rate of increase. Except for one NMNR with a slight decline, the conservation of remaining NMNRs was considered effective with increase varied from 14.8 % to 87.5 % in the level of protective efficacy. The conservation effectiveness of NMNRs was affected by both anthropogenic and natural factors, while the improvement to the conservation effectiveness was largely attributed to the implementation of protection policies, such as reforestation engineering. Further direct or indirect challenges in mangrove conservation effectiveness, e.g., pollution, natural disasters, and exotic species invasion, still require close attention. This study provides an effective and efficient approach to quantify the conservation effectiveness of mangrove nature reserves, which would facilitate mangrove conservation and management in the future.