41 results on '"Xiaokang Fu"'
Search Results
2. Social media space provides public surveillance for suicide: 10-year study in Japan using advanced deep learning models (Preprint)
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Siqin Wang, Huan Ning, Huang Xiao, Yunyu Xiao, Mengxi Zhang, Fan Yang, Yukio Sadahiro, Yan Liu, Zhenlong Li, Tao Hu, Xiaokang Fu, Zi Li, and Ye Zeng
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Health Informatics - Published
- 2023
3. Can social media space provide public surveillance for suicide? 10-year evidence from Japan (Preprint)
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Siqin Wang, Huan Ning, Huang Xiao, Yunyu Xiao, Mengxi Zhang, Fan Yang, Yukio Sadahiro, Yan Liu, Zhenlong Li, Tao Hu, Xiaokang Fu, Zi Li, and Ye Zeng
- Abstract
BACKGROUND Social media platforms have been increasingly used to express suicidal thoughts, feelings, and acts, raising public concerns over time. A large body of literature has explored the suicide risks identified by people’s expressions in social media space. However, there is less assertive to conclude that social media provides public surveillance for suicide without being able to align suicide risks detected in social media space with actual suicidal behaviours. Corroborating this alignment is a crucial foundation for suicide prevention and intervention through social media and for estimating and predicting suicide in countries with no reliable suicide statistics. OBJECTIVE This study aims to corroborate whether the suicide risks identified in social media space align with actual suicidal behaviours. This aim is achieved by tracking suicide risks detected by 62-million tweets posted in Japan over a 10-year period and assessing the locational and temporal alignment of such suicide risks with actual suicide behaviours, recorded in the national suicide statistics. METHODS This study utilizes a human-in-the-loop approach to identify suicide risk tweets posted in Japan in the period from January 2013 to December 2022. This approach involves keyword-filtered data mining, data scanning by human efforts, and data refinement via an advanced natural language processing model termed the Bidirectional Encoder Representations from Transformers. The tweets-identified suicide risks are then compared with actual suicide records in both temporal and spatial dimensions to validate if they are statistically correlated. RESULTS Twitter-identified suicide risks and actual suicide records are temporally correlated by month in the 10 years from 2013 to 2022 (correlation coefficient= 0.533; p CONCLUSIONS Social media platforms provide an anonymous space where people express their suicidal thoughts, ideation, and acts. Such expressions can serve as an alternative source to estimating and predicting suicide in countries without reliable suicide statistics. It can also provide real-time tracking of suicide risks, serving as the early warning for suicide committed. The identification of areas where suicide risks are highly concentrated is crucial for place-based mental health planning, enabling suicide prevention and intervention through social media in a spatially and temporally explicit manner. CLINICALTRIAL N/A
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- 2023
4. Revealing the Spatial Co-Occurrence Patterns of Multi-Emotions from Social Media Data
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Dongyang Wang, Yandong Wang, Xiaokang Fu, Mingxuan Dou, Shihai Dou, and Duocai Zhang
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- 2023
5. A Dof Transcription Factor Ghdof1.7 Plays a Positive Regulatory Role Under Salinity Stress in Upland Cotton
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Yi Li, Miaomiao Tian, Zhen Feng, Hengling Wei, Jingjing Zhang, Jianhua Lu, Xiaokang Fu, Liang Ma, Shuxun Yu, and Hantao Wang
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- 2023
6. Human mobility and COVID-19 transmission: a systematic review and future directions
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Mengxi Zhang, Siqin Wang, Tao Hu, Xiaokang Fu, Xiaoyue Wang, Yaxin Hu, Briana Halloran, Zhenlong Li, Yunhe Cui, Haokun Liu, Zhimin Liu, and Shuming Bao
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General Earth and Planetary Sciences ,Computer Science Applications - Abstract
Without a widely distributed vaccine, controlling human mobility has been identified and promoted as the primary strategy to mitigate the transmission of COVID-19. Many studies have reported the relationship between human mobility and COVID-19 transmission by utilizing the spatial-temporal information of mobility data from various sources. To better understand the role of human mobility in the pandemic, we conducted a systematic review of articles that measure the relationship between human mobility and COVID-19 in terms of their data sources, mathematical models, and key findings. Following the guidelines of the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) statement, we selected 47 articles from the Web of Science Core Collection up to September 2020. Restricting human mobility reduced the transmission of COVID-19, although the effectiveness and stringency of policy implementation vary temporally and spatially across different stages of the pandemic. We call for prompt and sustainable measures to control the pandemic. We also recommend researchers 1) to enhance multi-disciplinary collaboration; 2) to adjust the implementation and stringency of mobility-control policies in corresponding to the rapid change of the pandemic; 3) to improve mathematical models used in analysing, simulating, and predicting the transmission of the disease; and 4) to enrich the source of mobility data to ensure data accuracy and suability.
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- 2022
7. Study on spatial distribution of coalbed methane contents in coal seams based on key interpolation points: an example from Shizhuang South block in, Shanxi Province, China
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Yang Sen, Xiaoming Ni, Xiaokang Fu, Bin Xu, and Wenlong Zhou
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Fuel Technology ,General Chemical Engineering ,Energy Engineering and Power Technology ,General Chemistry ,Geotechnical Engineering and Engineering Geology - Published
- 2022
8. A Comprehensive Analysis of the DUF4228 Gene Family in
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Xiaoyan, Lv, Fei, Wei, Boying, Lian, Guo, Yin, Mengxi, Sun, Pengyun, Chen, Li, An, Hongliang, Jian, Hantao, Wang, Xiaokang, Fu, Liang, Ma, Jianhua, Lu, Baoquan, Wang, and Hengling, Wei
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Gossypium ,Stress, Physiological ,Gene Expression Regulation, Plant ,Multigene Family ,Salt Tolerance ,Phylogeny ,Plant Proteins - Abstract
Soil salinization conditions seriously restrict cotton yield and quality. Related studies have shown that the DUF4228 proteins are pivotal in plant resistance to abiotic stress. However, there has been no systematic identification and analysis of the DUF4228 gene family in cotton and their role in abiotic stress. In this study, a total of 308
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- 2022
9. A Comprehensive Gene Co-Expression Network Analysis Reveals a Role of
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Pengyun, Chen, Fei, Wei, Hongliang, Jian, Tingli, Hu, Baoquan, Wang, Xiaoyan, Lv, Hantao, Wang, Xiaokang, Fu, Shuxun, Yu, Hengling, Wei, and Liang, Ma
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Plant Breeding ,Gossypium ,Gene Expression Regulation, Plant ,Stress, Physiological ,Salt Stress ,Lipids ,Droughts ,Transcription Factors ,Peptide Hydrolases - Abstract
Abiotic stress, such as drought and salinity stress, seriously inhibit the growth and development of plants. Therefore, it is vital to understand the drought and salinity resistance mechanisms to enable cotton to provide more production under drought and salt conditions. In this study, we identified 8806 and 9108 differentially expressed genes (DEGs) through a comprehensive analysis of transcriptomic data related to the PEG-induced osmotic and salt stress in cotton. By performing weighted gene co-expression network analysis (WGCNA), we identified four co-expression modules in PEG treatment and five co-expression modules in salinity stress, which included 346 and 324 predicted transcription factors (TFs) in these modules, respectively. Correspondingly, whole genome duplication (WGD) events mainly contribute to the expansion of those TFs. Kyoto Encyclopedia of Genes and Genomes (KEGG) and gene ontology (GO) analyses revealed those different modules were associated with stress resistance, including regulating macromolecule metabolic process, peptidase activity, transporter activity, lipid metabolic process, and responses to stimulus. Quantitative RT-PCR analysis was used to confirm the expression levels of 15 hub TFs in PEG6000 and salinity treatments. We found that the hub gene
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- 2022
10. Systematic analysis of CNGCs in cotton and the positive role of GhCNGC32 and GhCNGC35 in salt tolerance
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Zhengying Lu, Guo Yin, Mao Chai, Lu Sun, Hengling Wei, Jie Chen, Yufeng Yang, Xiaokang Fu, and Shiyun Li
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Gossypium ,Gene Expression Regulation, Plant ,Stress, Physiological ,Genetics ,Cyclic Nucleotide-Gated Cation Channels ,Salt Tolerance ,Phylogeny ,Abscisic Acid ,Droughts ,Plant Proteins ,Biotechnology - Abstract
Background Cyclic nucleotide-gated ion channels (CNGCs) are calcium-permeable channels that participate in a variety of biological functions, such as signaling pathways, plant development, and environmental stress and stimulus responses. Nevertheless, there have been few studies on CNGC gene family in cotton. Results In this study, a total of 114 CNGC genes were identified from the genomes of 4 cotton species. These genes clustered into 5 main groups: I, II, III, IVa, and IVb. Gene structure and protein motif analysis showed that CNGCs on the same branch were highly conserved. In addition, collinearity analysis showed that the CNGC gene family had expanded mainly by whole-genome duplication (WGD). Promoter analysis of the GhCNGCs showed that there were a large number of cis-acting elements related to abscisic acid (ABA). Combination of transcriptome data and the results of quantitative RT–PCR (qRT–PCR) analysis revealed that some GhCNGC genes were induced in response to salt and drought stress and to exogenous ABA. Virus-induced gene silencing (VIGS) experiments showed that the silencing of the GhCNGC32 and GhCNGC35 genes decreased the salt tolerance of cotton plants (TRV:00). Specifically, physiological indexes showed that the malondialdehyde (MDA) content in gene-silenced plants (TRV:GhCNGC32 and TRV:GhCNGC35) increased significantly under salt stress but that the peroxidase (POD) activity decreased. After salt stress, the expression level of ABA-related genes increased significantly, indicating that salt stress can trigger the ABA signal regulatory mechanism. Conclusions we comprehensively analyzed CNGC genes in four cotton species, and found that GhCNGC32 and GhCNGC35 genes play an important role in cotton salt tolerance. These results laid a foundation for the subsequent study of the involvement of cotton CNGC genes in salt tolerance.
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- 2022
11. Spatiotemporal characteristics and factor analysis of SARS-CoV-2 infections among healthcare workers in Wuhan, China
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Peixiao Wang, Tao Hu, Hongqiang Liu, Hui Ren, Xinyan Zhu, and Xiaokang Fu
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Adult ,Male ,Microbiology (medical) ,China ,Physics - Physics and Society ,2019-20 coronavirus outbreak ,Health Personnel ,Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) ,education ,FOS: Physical sciences ,Physics and Society (physics.soc-ph) ,030501 epidemiology ,Healthcare worker infection ,Article ,Disease Outbreaks ,Geographical detector ,03 medical and health sciences ,Health personnel ,Spatio-Temporal Analysis ,Environmental health ,Health care ,Humans ,Medicine ,0303 health sciences ,SARS-CoV-2 ,030306 microbiology ,business.industry ,Central city ,COVID-19 ,Hospital level ,General Medicine ,Middle Aged ,Spatiotemporal pattern ,Occupational Diseases ,Infectious Diseases ,Infection sources ,Viral outbreak ,Female ,Factor analysis ,Factor Analysis, Statistical ,0305 other medical science ,business - Abstract
Studying the spatiotemporal distribution of SARS-CoV-2 infections among healthcare workers (HCWs) can aid in protecting them from exposure. Existing studies related to HCW infections have emphasized infection rates and protective measures. However, the spatiotemporal patterns and related external environmental factors of HCW infections remain unclear. To fill this gap, an open-source dataset of HCW diagnoses was provided, and the spatiotemporal distributions of SARS-CoV-2 infections among HCWs in Wuhan, China were explored. A geographical detector technique was then used to investigate the impacts of hospital level, type, distance from the infection source, and other external indicators of HCW infections. The results showed that the number of daily HCW infections over time in Wuhan followed a log-normal distribution, with and its mean observed on January 23, 2020 and a standard deviation of 10.8 days. The implementation of high-impact measures, such as the lockdown of the city, may have increased the probability of HCW infections in the short term, especially for HCWs in the outer ring of Wuhan. The infection of HCWs Wuhan exhibited clear spatial heterogeneity. The number of HCW infections was higher in the central city and lower in the outer city. Moreover, HCW infections displayed significant spatial autocorrelation and dependence. Factors analyses revealed that hospital level and type had an even greater impact on HCW infections; third-class and general hospitals closer to infection sources were correlated with especially high risks of infection. These findings can aid national epidemic prevention and control departments to understand the spatiotemporal distributions of viral transmission resulting in HCW infections, as well as external influencing factors, which can facilitate the protection of HCWs in China.
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- 2021
12. Cytokinin signaling localized in phloem noncell‐autonomously regulates cambial activity during secondary growth of Populus stems
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Xuelian Du, Shuai Liu, Changzheng Xu, Huili Su, Keming Luo, and Xiaokang Fu
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0106 biological sciences ,0301 basic medicine ,Cytokinins ,Physiology ,Secondary growth ,Plant Science ,Phloem ,Biology ,01 natural sciences ,03 medical and health sciences ,chemistry.chemical_compound ,heterocyclic compounds ,Cambium ,Transcription factor ,Gene knockdown ,fungi ,Histidine kinase ,food and beverages ,Cell biology ,Response regulator ,Populus ,030104 developmental biology ,chemistry ,Cytokinin ,Signal Transduction ,010606 plant biology & botany - Abstract
The regulation of cytokinin on secondary vascular development has been uncovered by modulating cytokinin content. However, it remains unclear how cytokinin enriched in developing secondary phloem regulates cambium activity in poplar. Here, we visualized the gradient distribution of cytokinin with a peak in the secondary phloem of poplar stem via immunohistochemical imaging, and determined the role of phloem-located cytokinin signaling during wood formation. We generated transgenic poplar harboring cytokinin oxidase/dehydrogenase (CKX)2, a gene encoding a cytokinin degrading enzyme, driven by the phloem-specific CLE41b promoter, indicating that the disruption of the cytokinin gradient pattern restricts the cambial activity. The RNA interference-based knockdown of the histidine kinase (HK) genes encoding cytokinin receptors specifically in secondary phloem significantly compromised the division activity of cambial cells, whereas the phloem-specific expression of a type-B response regulator (RR) transcription factor stimulated cambial proliferation, providing evidence for the noncell-autonomous regulation of local cytokinin signaling on the cambial activity. Moreover, the cambium-specific knockdown of HKs also led to restricted cambial activity, and the defects were aggravated by the reduced cytokinin accumulation. Our results showed that local cytokinin signaling in secondary phloem regulates cambial activity noncell-autonomously, and coordinately with its local signaling in cambium.
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- 2021
13. GhGAI interacts with GhAP1 and regulates flowering pathway in upland cotton
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Zhen Feng, Qi Zhang, Yi Li, Pengbo Hao, Hengling Wei, Xiaokang Fu, Jianhua Lu, Liang Ma, Shuxun Yu, and Hantao Wang
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Agronomy and Crop Science - Published
- 2023
14. Genome-wide identification of NF-YA gene family in cotton and the positive role of GhNF-YA10 and GhNF-YA23 in salt tolerance
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Xiaokang Fu, Liang Ma, Hengling Wei, Jianhua Lu, Shuxun Yu, Hantao Wang, Jingjing Zhang, and Qi Zhang
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Cyclopentanes ,02 engineering and technology ,Acetates ,Biology ,Genes, Plant ,Gossypium raimondii ,Biochemistry ,Genome ,Chromosomes, Plant ,Conserved sequence ,03 medical and health sciences ,Gene Expression Regulation, Plant ,Stress, Physiological ,Structural Biology ,Gene Duplication ,Gene family ,Gene silencing ,Gene Silencing ,Oxylipins ,Functional studies ,Nucleotide Motifs ,Selection, Genetic ,Promoter Regions, Genetic ,Molecular Biology ,Gene ,Conserved Sequence ,Phylogeny ,Plant Proteins ,030304 developmental biology ,Genetics ,Gossypium ,0303 health sciences ,Base Sequence ,Gene Expression Profiling ,Salt Tolerance ,General Medicine ,021001 nanoscience & nanotechnology ,Droughts ,Multigene Family ,Identification (biology) ,0210 nano-technology ,Genome, Plant ,Abscisic Acid - Abstract
Nuclear factor YA (NF-YA) genes play important roles in many biological processes, such as leaf growth, nitrogen nutrition, drought resistance, and salt stress. The functions of NF-YA genes in cotton have not been elucidated. The current study identified a total of 16, 16, 31, and 29 genes from Gossypium raimondii, G. arboretum, G. barbadense, and G. hirsutum, respectively. The NF-YA genes in cotton were phylogenetically classified into 4 groups. Analysis of gene structure, conserved motifs and multiple sequence alignments supported the evolutionary conservation of NF-YA family genes in cotton. Analysis of the expression patterns of GhNF-YAs in cotton suggested that GhNF-YAs play important roles in plant growth, development, and stress responses. The quantitative real-time PCR (qRT-PCR) validation of selected genes suggested that GhNF-YA genes are induced in response to salt, drought, ABA, and MeJA treatments. GhNF-YA genes may regulate salt and drought stress via the ABA or MeJA pathway. Silencing of GhNF-YA10 and GhNF-YA23 significantly reduced the salt tolerance of cotton seedlings, indicating that these genes participate in the regulation of the response of cotton to salt stress. These results establish a foundation for subsequent functional studies of the NF-YA gene family in cotton.
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- 2020
15. A Comprehensive Identification and Function Analysis of Serine/Arginine-Rich (SR) Proteins in Cotton (
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Fei, Wei, Pengyun, Chen, Hongliang, Jian, Lu, Sun, Xiaoyan, Lv, Hengling, Wei, Hantao, Wang, Tingli, Hu, Liang, Ma, Xiaokang, Fu, Jianhua, Lu, Shiyun, Li, and Shuxun, Yu
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Gossypium ,Gene Expression Regulation, Plant ,Stress, Physiological ,Multigene Family ,Serine ,Arginine ,Genome, Plant ,Phylogeny ,Plant Proteins - Abstract
As one of the most important factors in alternative splicing (AS) events, serine/arginine-rich (SR) proteins not only participate in the growth and development of plants but also play pivotal roles in abiotic stresses. However, the research about SR proteins in cotton is still lacking. In this study, we performed an extensive comparative analysis of SR proteins and determined their phylogeny in the plant lineage. A total of 169 SR family members were identified from four
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- 2022
16. A Sewing Line Planning Model Based on RFID Technology
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Jiangbo Zou, Xiaokang Fu, and Chunhua Ju
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Waiting time ,0209 industrial biotechnology ,Line planning ,Workstation ,Computer science ,02 engineering and technology ,Manufacturing systems ,Industrial engineering ,law.invention ,Product (business) ,020901 industrial engineering & automation ,law ,Genetic algorithm ,0202 electrical engineering, electronic engineering, information engineering ,Evaluated data ,020201 artificial intelligence & image processing ,Electrical and Electronic Engineering ,Line (text file) - Abstract
Sewing line is one of assembly lines in manufacturing systems in which a product is assembled progressively in workstations by different workers or machines, each executing a subset of the needed assembly tasks. Usually sewing line planning is based on experts’ evaluation of each procedure subjectively, leading to unnecessarily waiting time. To address this issue, in this article we propose a new model named adjustable sewing line planning (ASLP) model, in which both experts’ evaluated data and real-time data are leveraged to improve the line balance timely, along with a RFID based framework and a quadratic-selection genetic algorithm which are designed for line balance optimization. By conducting experiment on one of the largest garment manufacturing companies the model, it can be found from the results that the proposed model is efficient and promising.
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- 2020
17. Evaluation of coal reservoir coalbed methane production potential in considering different coal structures in a coal seam section: a case study of the Shizhuang North Block in the Qinshui Basin
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Xiaokang Fu, Bin Xu, Xuebin Tan, Yang Sen, and Xiaoming Ni
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Global and Planetary Change ,Coalbed methane ,Petroleum engineering ,business.industry ,technology, industry, and agriculture ,Coal mining ,Soil Science ,Geology ,respiratory system ,Structural basin ,complex mixtures ,Pollution ,respiratory tract diseases ,Permeability (earth sciences) ,Section (archaeology) ,otorhinolaryngologic diseases ,Environmental Chemistry ,Production (economics) ,Coal ,Geological Strength Index ,business ,Earth-Surface Processes ,Water Science and Technology - Abstract
Gas content and permeability are important parameters for the evaluation of coal reservoir gas production potential. When heterogeneity of these parameters is strong in a coal seam section, the results of any evaluation not considering the body of the coal structure and differences therein are quite different from reality. To this end, taking Shizhuang North Block 3# coal seam in Qinshui Basin as the research object, evaluation indices for CBM production potential considering different coal structure in a coal seam section were selected considering coalbed methane resource conditions, production power conditions, and removability conditions. Taking the geological strength index (GSI) as the link, the thickness, gas content, permeability, and brittleness index of different coal structures in a coal seam section were quantitatively characterized. Based on an analytical hierarchy process (AHP), a system for the evaluation of coal reservoir CBM production potential was constructed considering different coal structure in coal seam sections. The evaluation method was applied to Shizhuang north block in Qinshui Basin (Shanxi Province, China), and the results were compared with those obtained using the evaluation method without considering coal structure differences. The results show that when the heterogeneity of coal structure in a given coal seam section is strong, the evaluation of CBM production potential considering different coal structures can better reflect the objective facts, while in areas consisting of less heterogeneous coal structures, the results obtained using the proposed method differ slightly from those evaluated without considering such differences. The research findings provide a novel approach for accurately evaluating CBM production potential of coal reservoirs in areas consisting of highly heterogeneous coal structures.
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- 2021
18. Corrigendum: Genome-Wide Identification and Expression Pattern Analysis of the HAK/KUP/KT Gene Family of Cotton in Fiber Development and Under Stresses
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Xu Yang, Jingjing Zhang, Aimin Wu, Hengling Wei, Xiaokang Fu, Miaomiao Tian, Liang Ma, Jianhua Lu, Hantao Wang, and Shuxun Yu
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stress ,expression patterns ,HAK/KUP/KT ,fiber development ,Genetics ,Molecular Medicine ,QH426-470 ,cotton ,Genetics (clinical) - Published
- 2021
19. Non-functional GoFLA19s are responsible for the male sterility caused by hybrid breakdown in cotton (Gossypium spp.)
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Ji Liu, Qiang Ma, Liang Ma, Hengling Wei, Yingjie Bian, Guangzhi Mao, Hantao Wang, Meng Zhang, Jingjing Zhang, Xiaokang Fu, Aimin Wu, Pengyun Chen, and Shuxun Yu
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Genetics ,Gossypium ,Plant Infertility ,Sterility ,Mutant ,Stamen ,Sequence alignment ,Cell Biology ,Plant Science ,Gossypium barbadense ,Flowers ,Biology ,Plants, Genetically Modified ,Chromosomes, Plant ,Tetraploidy ,Mucoproteins ,Arabinogalactan ,Gene Expression Regulation, Plant ,Loss of Function Mutation ,Pollen ,CRISPR-Cas Systems ,Gene ,Arabinogalactan protein ,Plant Proteins - Abstract
Hybrid breakdown (HB) functions as a common reproductive barrier and reduces hybrid fitness in many species, including cotton. However, the related genes and the underlying genetic mechanisms of HB in cotton remain unknown. Here, we found that the photosensitive genetic male sterile line CCRI9106 was a hybrid progeny of Gossypium hirsutum and Gossypium barbadense and probably a product of HB. Fine mapping with F2 s (CCRI9106 × G. hirsutum/G. barbadense lines) identified a pair of male sterility genes GoFLA19s (encoding fasciclin-like arabinogalactan family protein) located on chromosomes A12 and D12. Crucial variations occurring in the fasciclin-like domain and the arabinogalactan protein domain were predicted to cause the non-functionalization of GbFLA19-D and GhFLA19-A. CRISPR/Cas9-mediated knockout assay confirmed the effects of GhFLA19s on male sterility. Sequence alignment analyses showed that variations in GbFLA19-D and GhFLA19-A likely occurred after the formation of allotetraploid cotton species. GoFLA19s are specifically expressed in anthers and contribute to tapetal development, exine assembly, intine formation, and pollen grain maturation. RNA-sequencing and quantitative reverse transcriptase-polymerase chain reaction analyses illustrated that genes related to these biological processes were significantly downregulated in the mutant. Our research on male sterility genes, GoFLA19s, improves the understanding of the molecular characteristics and evolutionary significance of HB in interspecific hybrid breeding.
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- 2021
20. GhGPAT12/25 Are Essential for the Formation of Anther Cuticle and Pollen Exine in Cotton (Gossypium hirsutum L.)
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Jingjing Zhang, Xiaokang Fu, Meng Zhang, Aimin Wu, Jianhua Lu, Hantao Wang, Pengbo Hao, Shuxun Yu, Liang Ma, Hengling Wei, and Qiang Ma
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anther cuticle ,Tapetum ,GhGPAT12/25 ,Sterility ,Cuticle ,Mutant ,Stamen ,Plant culture ,Plant Science ,pollen exine ,Biology ,male sterility ,medicine.disease_cause ,cotton ,SB1-1110 ,Cell biology ,Microspore ,Pollen ,medicine ,CRISPR/Cas9 ,Gene ,Original Research - Abstract
Glycerol-3-phosphate acyltransferases (GPATs), critical for multiple biological processes like male fertility, have been extensively characterized. However, their precise functions and underlying regulatory mechanism in cotton anther development are unclear. This research demonstrated the importance of GhGPAT12/25 (a paralogs pair on A12/D12 sub-chromosome of cotton) to regulate the degradation of tapetum, anther cuticle formation, and pollen exine development. GhGPAT12 and GhGPAT25 exhibited specifically detected transcripts in tapetum and pollen exine during the early anther developmental stages. GhGPAT12/25 are sn-2 glycerol-3-phosphate acyltransferases and can transfer the acyl group of palmitoyl-CoA to glycerol-3-phosphate (G3P). CRISPR/Cas9-mediated knockout identified the functional redundancy of GhGPAT12 and GhGPAT25. Knockout of both genes caused completely male sterility associated with abnormal anther cuticle, swollen tapetum, and inviable microspores with defective exine and irregular unrestricted shape. RNA-seq analysis showed that the loss of function of GhGPAT12/25 affects the processes of wax metabolic, glycerol monomer biosynthesis, and transport. Consistently, cuticular waxes were dramatically reduced in mutant anthers. Yeast one-hybrid system (Y1H), virus-induced gene silencing (VIGS), and dual-luciferase (LUC) assays illustrated that GhMYB80s are likely to directly activate the expression of GhGPAT12/25. This study provides important insights for revealing the regulatory mechanism underlying anther development in cotton.
- Published
- 2021
21. QTL mapping and candidate gene identification of lint percentage based on a recombinant inbred line population of upland cotton
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Xiaokang Fu, Xiaoyun Jia, Hengling Wei, Meng Kang, Shuxun Yu, Hantao Wang, Liang Ma, Jianhua Lu, and Wei Li
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0106 biological sciences ,0301 basic medicine ,Genetics ,Nonsynonymous substitution ,education.field_of_study ,Lint ,Candidate gene ,Population ,Single-nucleotide polymorphism ,Plant Science ,Horticulture ,Biology ,Quantitative trait locus ,Candidate Gene Identification ,01 natural sciences ,03 medical and health sciences ,030104 developmental biology ,education ,Agronomy and Crop Science ,010606 plant biology & botany ,Genetic association - Abstract
Lint percentage is a major yield component in cotton breeding programmes. To identify quantitative trait loci (QTLs) and candidate genes related to lint percentage, we used an intraspecific recombinant inbred line population of 137 lines derived from Gossypium hirsutum cv. CCRI36 and G. hirsutum acc. G2005 for QTL mapping of lint percentage. Based on a high-density genetic map and phenotype data collected in four growing environments, we identified a total of 28 QTLs for lint percentage. Three stable QTLs (qLP-At5-2, qLP-Dt7-1 and qLP-Dt7-2) were detected in at least two environments. Two genes (Gh_A05G1584 and Gh_A05G1689) containing nonsynonymous single nucleotide polymorphisms (SNPs) were identified by association analysis using published data. The quantitative real-time PCR results showed that the expression levels of Gh_A05G1584 were higher in cv. CCRI36 than in acc. G2005 during all fibre development stages; Gh_A05G1689 was mainly expressed in 15 and 25 days post-anthesis fibres and its expression level was higher in cv. CCRI36. These results suggest candidate genes for lint percentage and provide molecular information for use in cotton breeding programmes aimed at improving yield.
- Published
- 2021
22. Understanding the topic evolution of scientific literatures like an evolving city: Using Google Word2Vec model and spatial autocorrelation analysis
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Jie Zheng, Kai Hu, Huayi Wu, Jin Mao, Zhu Qibing, Kunlun Qi, Siluo Yang, Qing Luo, Ya Guo, and Xiaokang Fu
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Computer science ,05 social sciences ,Library and Information Sciences ,Management Science and Operations Research ,050905 science studies ,Semantics ,Popularity ,Data science ,Field (geography) ,Computer Science Applications ,Semantic similarity ,Media Technology ,Word2vec ,Language model ,0509 other social sciences ,050904 information & library sciences ,Citation ,Spatial analysis ,Information Systems - Abstract
Topic evolution has been described by many approaches from a macro level to a detail level, by extracting topic dynamics from text in literature and other media types. However, why the evolution happens is less studied. In this paper, we focus on whether and how the keyword semantics can invoke or affect the topic evolution. We assume that the semantic relatedness among the keywords can affect topic popularity during literature surveying and citing process, thus invoking evolution. However, the assumption is needed to be confirmed in an approach that fully considers the semantic interactions among topics. Traditional topic evolution analyses in scientometric domains cannot provide such support because of using limited semantic meanings. To address this problem, we apply the Google Word2Vec, a deep learning language model, to enhance the keywords with more complete semantic information. We further develop the semantic space as an urban geographic space. We analyze the topic evolution geographically using the measures of spatial autocorrelation, as if keywords are the changing lands in an evolving city. The keyword citations (keyword citation counts one when the paper containing this keyword obtains a citation) are used as an indicator of keyword popularity. Using the bibliographical datasets of the geographical natural hazard field, experimental results demonstrate that in some local areas, the popularity of keywords is affecting that of the surrounding keywords. However, there are no significant impacts on the evolution of all keywords. The spatial autocorrelation analysis identifies the interaction patterns (including High-High leading, High-Low suppressing) among the keywords in local areas. This approach can be regarded as an analyzing framework borrowed from geospatial modeling. Moreover, the prediction results in local areas are demonstrated to be more accurate if considering the spatial autocorrelations.
- Published
- 2019
23. Dual Reproductive Cell-Specific Promoter-Mediated Split-Cre/LoxP System Suitable for Exogenous Gene Deletion in Hybrid Progeny of Transgenic
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Xiaokang Fu, Jia Ge, Changzheng Xu, Keming Luo, and Chen Yang
- Subjects
0106 biological sciences ,0301 basic medicine ,QH301-705.5 ,Transgene ,Genetic Vectors ,Arabidopsis ,Cre/LoxP ,Cre recombinase ,Genetically modified crops ,Biology ,01 natural sciences ,Catalysis ,Article ,Inorganic Chemistry ,03 medical and health sciences ,Gene Expression Regulation, Plant ,Transgenes ,Biology (General) ,Physical and Theoretical Chemistry ,Promoter Regions, Genetic ,QD1-999 ,Molecular Biology ,Gene ,Spectroscopy ,Genetics ,Recombination, Genetic ,Reporter gene ,Expression vector ,Integrases ,hybrid ,Arabidopsis Proteins ,Reproduction ,Organic Chemistry ,biosafety ,Promoter ,General Medicine ,Plants, Genetically Modified ,Computer Science Applications ,Chemistry ,030104 developmental biology ,reproductive cell specificity ,Cre-Lox recombination ,Genetic Engineering ,Gene Deletion ,010606 plant biology & botany - Abstract
Genetically modified (GM) crops possess some superior characteristics, such as high yield and insect resistance, but their biosafety has aroused broad public concern. Some genetic engineering technologies have recently been proposed to remove exogenous genes from GM crops. Few approaches have been applied to maintain advantageous traits, but excising exogenous genes in seeds or fruits from these hybrid crops has led to the generation of harvested food without exogenous genes. In a previous study, split-Cre mediated by split intein could recombine its structure and restore recombination activity in hybrid plants. In the current study, the recombination efficiency of split-Cre under the control of ovule-specific or pollen-specific promoters was validated by hybridization of transgenic Arabidopsis containing the improved expression vectors. In these vectors, all exogenous genes were flanked by two loxP sites, including promoters, resistance genes, reporter genes, and split-Cre genes linked to the reporter genes via LP4/2A. A gene deletion system was designed in which NCre was driven by proDD45, and CCre was driven by proACA9 and proDLL. Transgenic lines containing NCre were used as paternal lines to hybridize with transgenic lines containing CCre. Because this hybridization method results in no co-expression of the NCre and CCre genes controlled by reproduction-specific promoters in the F1 progeny, the desirable characteristics could be retained. After self-crossing in F1 progeny, the expression level and protein activity of reporter genes were detected, and confirmed that recombination of split-Cre had occurred and the exogenous genes were partially deleted. The gene deletion efficiency represented by the quantitative measurements of GUS enzyme activity was over 59%, with the highest efficiency of 73% among variable hybrid combinations. Thus, in the present study a novel dual reproductive cell-specific promoter-mediated gene deletion system was developed that has the potential to take advantage of the merits of GM crops while alleviating biosafety concerns.
- Published
- 2021
24. Comprehensive Identification and Expression Analysis of the Members of the B-Box Gene Family of Cotton Involved in Flower bud Differentiation and Responses to Multiple Stresses
- Author
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Jianhua Lu, Mengyu Li, Hengling Wei, Shuxun Yu, Xu Yang, Yi Li, Liang Ma, Wang Hantao, Zhen Feng, and Xiaokang Fu
- Subjects
Genetics ,Bud ,Expression analysis ,Gene family ,Identification (biology) ,Biology - Abstract
Background: B-BOX (BBX) proteins are zinc-finger transcription factors with one or two BBX domains and sometimes a CCT domain. These proteins play an essential role in regulating plant growth and development, as well as in resisting abiotic stress. So far, the BBX gene family has been widely studied in other crops. However, no one has systematically studied the BBX gene in cotton. Results: In the present study, 17, 18, 37 and 33 BBX genes were detected in Gossypium arboreum, G. raimondii, G. hirsutum and G. barbadense, respectively, via genome-wide identification. Phylogenetic analysis showed that all BBX genes were divided into 5 main categories. The protein motifs and exon/intron structures indicated that each group of BBX genes was highly conserved. Collinearity analysis revealed that the amplification of BBX gene family in Gossypium spp. was mainly through segmental replication. Nonsynonymous (Ka)/ synonymous (Ks) substitution ratios indicated that the BBX gene family had undergone purification selection throughout the long-term natural selection process. Moreover, transcriptomic data showed that some GhBBX genes were highly expressed in floral organs. Transcriptome data analysis and qRT-PCR verification showed that different GhBBX genes had different biological functions in flower bud differentiation, abiotic stress and stress response. Conclusions: Our comprehensive analysis of BBX in G. hirsutum provides a basis for further study on the molecular role of GhBBXs in regulating flowering and cotton resistance to abiotic stress.
- Published
- 2021
25. Human mobility and COVID-19 transmission: a systematic review and future directions
- Author
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Yaxin Hu, Xiaoyue Wang, Briana Halloran, Siqin Wang, Shuming Bao, Tao Hu, Haokun Liu, Yunhe Cui, Mengxi Zhang, Zhimin Liu, and Xiaokang Fu
- Subjects
Systematic review ,Web of science ,Coronavirus disease 2019 (COVID-19) ,Risk analysis (engineering) ,Transmission (telecommunications) ,Computer science ,Control (management) ,Pandemic ,Key (cryptography) ,Statistical model - Abstract
Without a widely distributed vaccine, controlling human mobility has been identified and promoted as the primary strategy to mitigate the transmission of COVID-19. Many studies have reported the relationship between human mobility and COVID-19 transmission by utilizing the spatial-temporal information of mobility data from various sources. To better understand the role of human mobility in the pandemic, we conducted a systematic review of articles that measure the relationship between human mobility and COVID-19 in terms of their data sources, statistical models, and key findings. Following the guidelines of the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) statement, we selected 47 articles from Web of Science Core Collection up to September 2020. Restricting human mobility reduced the transmission of COVID-19 spatially, although the effectiveness and stringency of policy implementation vary temporally and spatially across different stages of the pandemic. We call for prompt and sustainable measures to control the pandemic. We also recommend researchers 1) to enhance multi-disciplinary collaboration; 2) to adjust the implementation and stringency of mobility-control policies in corresponding to the rapid change of the pandemic; 3) to improve statistical models used in analyzing, simulating, and predicting the transmission of the disease; and 4) to enrich the source of mobility data to ensure data accuracy and suability.
- Published
- 2021
26. Human Mobility Data in the COVID-19 Pandemic: Characteristics, Applications, and Challenges
- Author
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Bing She, Yaxin Hu, Xinyan Zhu, Siqin Wang, Xiaokang Fu, Xiaoyue Wang, Yunhe Cui, Peixiao Wang, Wendy Guan, Mengxi Zhang, Xiao Huang, Jacob Khuri, Zhenlong Li, Shuming Bao, and Tao Hu
- Subjects
Information privacy ,medicine.medical_specialty ,Coronavirus disease 2019 (COVID-19) ,business.industry ,Computer science ,media_common.quotation_subject ,Public health ,Data science ,Open data ,Mobile phone ,Public transport ,Pandemic ,medicine ,Quality (business) ,business ,media_common - Abstract
The COVID-19 pandemic poses unprecedented challenges around the world. Many studies indicate that human mobility data provide significant support for public health actions during the pandemic. Researchers have applied mobility data to explore spatiotemporal trends over time, investigate associations with other variables, and predict or simulate the spread of COVID-19. Our objective was to provide a comprehensive overview of human mobility open data to guide researchers and policymakers in conducting data-driven evaluations and decision-making for the COVID-19 pandemic and other infectious disease outbreaks. We summarized the mobility data usage in COVID-19 studies by reviewing recent publications on COVID-19 and human mobility from a data-oriented perspective. We identified three major sources of mobility data: public transit systems, mobile operators, and mobile phone applications. Four approaches have been commonly used to estimate human mobility: public transit-based flow, social activity patterns, index-based mobility data, and social media-derived mobility data. We compared mobility datasets’ characteristics by assessing data privacy, quality, space-time coverage, high-performance data storage and processing, and accessibility. We also present challenges and future directions of using mobility data. This review makes a pivotal contribution to understanding the use of and access to human mobility data in the COVID-19 pandemic and future disease outbreaks.
- Published
- 2021
27. The microRNA476a-RFL module regulates adventitious root formation through a mitochondria-dependent pathway in Populus
- Author
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Vincent L. Chiang, Xianqiang Wang, Jian Hu, Xiaokang Fu, Chaofeng Li, Keming Luo, Changzheng Xu, Haitao Xing, Yuanxun Tao, Li Guo, Ziwei Yang, Di Fan, and Huili Su
- Subjects
0106 biological sciences ,0301 basic medicine ,Physiology ,Regulator ,Morphogenesis ,Plant Science ,Mitochondrion ,Biology ,01 natural sciences ,Plant Roots ,03 medical and health sciences ,Auxin ,Gene Expression Regulation, Plant ,Gene ,Root formation ,chemistry.chemical_classification ,Indoleacetic Acids ,fungi ,Cell biology ,Mitochondria ,Plant Breeding ,030104 developmental biology ,Populus ,chemistry ,Pentatricopeptide repeat ,Developmental plasticity ,010606 plant biology & botany - Abstract
For woody plants, clonal propagation efficiency is largely determined by adventitious root (AR) formation at the bases of stem cuttings. However, our understanding of the molecular mechanisms contributing to AR morphogenesis in trees remains limited, despite the importance of vegetative propagation, currently the most common practice for tree breeding and commercialization. Here, we identified Populus-specific miR476a as a regulator of wound-induced adventitious rooting that acts by orchestrating mitochondrial homeostasis. MiR476a exhibited inducible expression during AR formation and directly targeted several Restorer of Fertility like (RFL) genes encoding mitochondrion-localized pentatricopeptide repeat proteins. Genetic modification of miR476a-RFL expression revealed that miR476a/RFL-mediated dynamic regulation of mitochondrial homeostasis influences AR formation in poplar. Mitochondrial perturbation via exogenous application of a chemical inhibitor indicated that miR476a/RFL-directed AR formation depends on mitochondrial regulation that acts via auxin signaling. Our results thus establish a microRNA-directed mitochondrion-auxin signaling cascade required for AR development, providing insights into the role of mitochondrial regulation in the developmental plasticity of plants.
- Published
- 2020
28. Assessing Reliability of Chinese Geotagged Social Media Data for Spatiotemporal Representation of Human Mobility
- Author
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Lingbo Liu, Ru Wang, Weihe Wendy Guan, Shuming Bao, Hanchen Yu, Xiaokang Fu, and Hongqiang Liu
- Subjects
human mobility ,social media ,geotagged ,Sina Weibo ,Baidu Qianxi ,LBS ,Geography, Planning and Development ,Earth and Planetary Sciences (miscellaneous) ,Computers in Earth Sciences - Abstract
Understanding the space-time dynamics of human activities is essential in studying human security issues such as climate change impacts, pandemic spreading, or urban sustainability. Geotagged social media posts provide an open and space-time continuous data source with user locations which is convenient for studying human movement. However, the reliability of Chinese geotagged social media data for representing human mobility remains unclear. This study compares human movement data derived from the posts of Sina Weibo, one of the largest social media software in China, and that of Baidu Qianxi, a high-resolution human movement dataset from ‘Baidu Map’, a popular location-based service in China with 1.3 billion users. Correlation analysis was conducted from multiple dimensions of time periods (weekly and monthly), geographic scales (cities and provinces), and flow directions (inflow and outflow), and a case study on COVID-19 transmission was further explored with such data. The result shows that Sina Weibo data can reveal similar patterns as that of Baidu Qianxi, and that the correlation is higher at the provincial level than at the city level and higher at the monthly scale than at the weekly scale. The study also revealed spatial variations in the degree of similarity between the two sources. Findings from this study reveal the values and properties and spatiotemporal heterogeneity of human mobility data extracted from Weibo tweets, providing a reference for the proper use of social media posts as the data sources for human mobility studies.
- Published
- 2022
29. Genome-wide identification and expression patterns analysis of the RPD3/HDA1 gene family in cotton
- Author
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Miaomiao Tian, Jingjing Zhang, Xiaokang Fu, Shuxun Yu, Pengbo Hao, Hengling Wei, Aimin Wu, Liang Ma, Shuaishuai Cheng, Qi Zhang, Hantao Wang, and Xu Yang
- Subjects
lcsh:QH426-470 ,lcsh:Biotechnology ,Histone Deacetylase 1 ,Flowers ,Expression patterns ,Gossypium raimondii ,Gossypium ,Genome ,Histone deacetylases ,Gene Expression Regulation, Plant ,Stress, Physiological ,lcsh:TP248.13-248.65 ,Genetics ,Early maturity ,Gene family ,Gene ,Plant Proteins ,biology ,Abiotic stress ,biology.organism_classification ,lcsh:Genetics ,Histone ,Multigene Family ,biology.protein ,DNA microarray ,Research Article ,Biotechnology - Abstract
Background Histone deacetylases (HDACs) catalyze histone deacetylation and suppress gene transcription during various cellular processes. Within the superfamily of HDACs, RPD3/HDA1-type HDACs are the most studied, and it is reported that RPD3 genes play crucial roles in plant growth and physiological processes. However, there is a lack of systematic research on the RPD3/HDA1 gene family in cotton. Results In this study, genome-wide analysis identified 9, 9, 18, and 18 RPD3 genes in Gossypium raimondii, G. arboreum, G. hirsutum, and G. barbadense, respectively. This gene family was divided into 4 subfamilies through phylogenetic analysis. The exon-intron structure and conserved motif analysis revealed high conservation in each branch of the cotton RPD3 genes. Collinearity analysis indicated that segmental duplication was the primary driving force during the expansion of the RPD3 gene family in cotton. There was at least one presumed cis-element related to plant hormones in the promoter regions of all GhRPD3 genes, especially MeJA- and ABA-responsive elements, which have more members than other hormone-relevant elements. The expression patterns showed that most GhRPD3 genes had relatively high expression levels in floral organs and performed higher expression in early-maturity cotton compared with late-maturity cotton during flower bud differentiation. In addition, the expression of GhRPD3 genes could be significantly induced by one or more abiotic stresses as well as exogenous application of MeJA or ABA. Conclusions Our findings reveal that GhRPD3 genes may be involved in flower bud differentiation and resistance to abiotic stresses, which provides a basis for further functional verification of GhRPD3 genes in cotton development and a foundation for breeding better early-maturity cotton cultivars in the future.
- Published
- 2020
30. The MicroRNA390/TRANS-ACTING SHORT INTERFERING RNA3 Module Mediates Lateral Root Growth under Salt Stress via the Auxin Pathway
- Author
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Li Guo, Yun Shen, Fu He, Changzheng Xu, Xiaokang Fu, Keming Luo, and Mi Leng
- Subjects
0106 biological sciences ,0301 basic medicine ,chemistry.chemical_classification ,Regulation of gene expression ,Gene knockdown ,Physiology ,fungi ,Lateral root ,food and beverages ,Repressor ,Plant Science ,01 natural sciences ,Cell biology ,03 medical and health sciences ,030104 developmental biology ,chemistry ,Auxin ,RNA interference ,Genetics ,Trans-acting ,Signal transduction ,010606 plant biology & botany - Abstract
Salt-induced developmental plasticity in a plant root system strongly depends on auxin signaling. However, the molecular events underlying this process are poorly understood. MicroRNA390 (miR390), trans-actin small interfering RNAs (tasiRNAs), and AUXIN RESPONSE FACTORs (ARFs) form a regulatory module involved in controlling lateral root (LR) growth. Here, we found that miR390 expression was strongly induced by exposure to salt during LR formation in poplar (Populus spp.) plants. miR390 overexpression stimulated LR development and increased salt tolerance, whereas miR390 knockdown caused by a short tandem target mimic repressed LR growth and compromised salt resistance. ARF3.1, ARF3.2, and ARF4 expression was inhibited significantly by the presence of salt, and transcript abundance was decreased dramatically in the miR390-overexpressing line but increased in the miR390-knockdown line. Constitutive expression of ARF4m harboring mutated trans-acting small interfering ARF-binding sites removed the salt resistance of the miR390 overexpressors. miR390 positively regulated auxin signaling in LRs subjected to salt, but ARF4 inhibited auxin signaling. Salinity stabilized the poplar Aux/IAA repressor INDOLE-3-ACETIC ACID17.1, and overexpression of an auxin/salt-resistant form of this repressor suppressed LR growth in miR390-overexpressing and ARF4-RNA interfering lines in the presence of salt. Thus, the miR390/TAS3/ARFs module is a key regulator, via modulating the auxin pathway, of LR growth in poplar subjected to salt stress.
- Published
- 2018
31. A comprehensive identification and function analysis of the ATBS1 Interacting Factors (AIFs) gene family of Gossypium species in fiber development and under multiple stresses
- Author
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Xiaokang Fu, Jingjing Zhang, Mengyu Li, Hantao Wang, Aimin Wu, Shuxun Yu, Xu Yang, Meng Zhang, Pengbo Hao, and Hengling Wei
- Subjects
Genetics ,Candidate gene ,biology ,Phylogenetic tree ,Abiotic stress ,Gossypium barbadense ,Gossypium ,biology.organism_classification ,Gossypium raimondii ,Gene family ,cardiovascular diseases ,biological phenomena, cell phenomena, and immunity ,Agronomy and Crop Science ,Gene - Abstract
ATBS1 INTERACTING FACTORs (AIFs) are atypical basic helix-loop-helix (bHLH) proteins play important roles in the growth and development of plants. There are no comprehensive reports on the genomic identification and functional analysis of AIFs in cotton. In this study, 8, 11, 16, and 15 AIFs were identified in Gossypium arboreum L., Gossypium raimondii L., Gossypium hirsutum L., and Gossypium barbadense L., respectively. AIFs were also screened in other species: 3 in Theobroma cacao L., 4 in Populus trichocarpa C. and 5 in Zea mays L. Based on a neighbour-joining phylogenetic tree, 66 AIF proteins identified in these species were divided into 3 groups. Multiple sequence alignment analysis showed that the AIF protein sequences were relatively conserved. Analysis of gene chromosome position and gene replication showed that AIFs amplification in cotton might be due to fragment and tandem replication. And cold stress response and plant hormone cis-elements were identified in the promoter regions of GhAIFs. Published transcriptional data showed that GhAIFs were differentially expressed in various tissues, especially in floral organs and fibers. qRT-PCR results showed that most of GhAIFs were highly expressed at the fiber initiation stage. Analysis of the expression of selected GhAIFs under abiotic stress (GA, IAA, SA, ABA, and 4 °C treatment) suggested that GhAIFs might be involved in the regulation of abiotic stress. The comprehensive analysis of the AIF gene family in upland cotton provides a foundation for further studies on the function of atypical bHLH-GhAIFs family members and screening of fiber development, and stress-resistant candidate genes in cotton.
- Published
- 2021
32. Response to immunotherapy in a patient with anaplastic thyroid cancer
- Author
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Yaxuan Zhang, Meng Wang, Yunhan Ma, Jian Zhu, Luming Zheng, Yanchen Li, Xiaokang Fu, Qingqing He, and Ling Li
- Subjects
Oncology ,medicine.medical_specialty ,Chemotherapy ,business.industry ,medicine.medical_treatment ,General Medicine ,Pembrolizumab ,Immunotherapy ,medicine.disease ,Malignancy ,chemistry.chemical_compound ,chemistry ,Internal medicine ,medicine ,Biomarker (medicine) ,Apatinib ,Anaplastic thyroid cancer ,business ,Thyroid cancer - Abstract
Rationale Anaplastic thyroid carcinoma (ATC) is an aggressive malignancy that is almost always fatal and lacks effective systemic treatment options. Current treatments of ATC include surgery, radiation, and chemotherapy, used in combination when possible. In the aspect of immunotherapy, the biomarker of TMB-H and MSI-H may suggest that patients benefit from pembrolizumab. Programmed cell death-ligand 1 (PD-L1) is highly expressed in ATC but has not been written into the guidelines or approved by the FDA as a biomarker for thyroid cancer immunotherapy. Patient concerns A 55-year-old woman was admitted to our hospital because of a slight right-sided neck enlargement in November 2019. Diagnoses The clinical diagnosis was ATC, pT3bN0M0, and stage IVB. Interventions Oral administration of apatinib (250 mg 3 times daily) was initiated after surgery, but some unpleasant side effects emerged after 1 month of treatment. Next-generation sequencing revealed that the tumor harbored 2 mutations, HRAS p.Q61R and TP53 p.P278S, and PD-L1 staining was positive with a high expression. Thus, camrelizumab (programmed cell death protein 1 inhibitor) was combined with apatinib, and apatinib was changed to 250 mg once a day from March 2020. Outcomes No adverse reactions were observed after the treatment immunotherapy combined with antiangiogenic drugs. Currently, the survival time of patients is more than 11 months, and the quality of life is not affected. Conclusion This case suggests that immunotherapy in patients with ATC based upon PD-L1 evaluation provides a therapeutic option. Targeting programmed cell death protein 1/PD-L1 may provide a much-needed treatment option for patients with advanced ATC.
- Published
- 2021
33. A Bibliometric Analysis and Network Visualisation of Human Mobility Studies from 1990 to 2020: Emerging Trends and Future Research Directions
- Author
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Zhe Gao, Siqin Wang, Yan Liu, Mengxi Zhang, Xiaokang Fu, Tao Hu, and Briana Halloran
- Subjects
Bibliometric analysis ,literature review ,VOSviewer ,Geography, Planning and Development ,Big data ,0507 social and economic geography ,TJ807-830 ,Management, Monitoring, Policy and Law ,network visualisation ,CiteSpace ,TD194-195 ,Renewable energy sources ,bibliometric analysis ,Modelling methods ,Health science ,0502 economics and business ,human mobility ,GE1-350 ,050210 logistics & transportation ,Environmental effects of industries and plants ,Renewable Energy, Sustainability and the Environment ,business.industry ,Deep learning ,05 social sciences ,Data science ,Visualization ,Environmental sciences ,Artificial intelligence ,business ,050703 geography - Abstract
Studies on human mobility have a long history with increasingly strong interdisciplinary connections across social science, environmental science, information and technology, computer science, engineering, and health science. However, what is lacking in the current research is a synthesis of the studies to identify the evolutional pathways and future research directions. To address this gap, we conduct a systematic review of human mobility-related studies published from 1990 to 2020. Drawing on the selected publications retrieved from the Web of Science, we provide a bibliometric analysis and network visualisation using CiteSpace and VOSviewer on the number of publications and year published, authors and their countries and afflictions, citations, topics, abstracts, keywords, and journals. Our findings show that human mobility-related studies have become increasingly interdisciplinary and multi-dimensional, which have been strengthened by the use of the so-called ‘big data’ from multiple sources, the development of computer technologies, the innovation of modelling approaches, and the novel applications in various areas. Based on our synthesis of the work by top cited authors we identify four directions for future research relating to data sources, modelling methods, applications, and technologies. We advocate for more in-depth research on human mobility using multi-source big data, improving modelling methods and integrating advanced technologies including artificial intelligence, and machine and deep learning to address real-world problems and contribute to social good.
- Published
- 2021
34. PtoMYB170 positively regulates lignin deposition during wood formation in poplar and confers drought tolerance in transgenic Arabidopsis
- Author
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Qiaoyan Tian, Bo Jiao, Keming Luo, Rui Liu, Xiaokang Fu, Li Guo, Lingyu Ran, Chaofeng Li, Bangjun Wang, and Changzheng Xu
- Subjects
0106 biological sciences ,0301 basic medicine ,Physiology ,Transgene ,Drought tolerance ,Arabidopsis ,Plant Science ,Genetically modified crops ,Lignin ,01 natural sciences ,03 medical and health sciences ,chemistry.chemical_compound ,Gene Expression Regulation, Plant ,Guard cell ,Botany ,Promoter Regions, Genetic ,biology ,Gene Expression Profiling ,fungi ,food and beverages ,Xylem ,Plants, Genetically Modified ,biology.organism_classification ,Wood ,Droughts ,Populus ,030104 developmental biology ,chemistry ,Heterologous expression ,010606 plant biology & botany - Abstract
Wood formation is a complex developmental process under multi-level transcriptional control executed by a large set of transcription factors. However, only limited members have been characterized to be key regulators of lignin biosynthesis in poplar. Here we report the conserved and unique functions of PtoMYB170, a transcription factor identified from Populus tomentosa (Chinese white poplar), in lignin deposition and drought tolerance in comparison with its duplicate paralog PtoMYB216. PtoMYB170 is preferentially expressed in young leaves and xylem tissues. Overexpression of PtoMYB170 in transgenic poplar plants resulted in stronger lignification and more thickened secondary wall in xylem compared with wild-type plants, whereas the CRISPR/Cas9-generated mutation of PtoMYB170 weakened lignin deposition, thereby leading to a more flexible and collapsed xylem phenotype. Transient expression experiments demonstrated that PtoMYB170 specifically activated the expression of lignin biosynthetic genes, consistent with the function of PtoMYB216. However, GUS staining assays revealed that PtoMYB170 was specifically expressed in guard cells of transgenic Arabidopsis while PtoMYB216 was not. Heterologous expression of PtoMYB170 in Arabidopsis enhanced stomatal closure in the dark and resulted in drought tolerance of the transgenic plants through reduced water loss, indicating a diversified role from PtoMYB216. These results revealed the PtoMYB170-dependent positive transcriptional regulation on lignin deposition in poplar and its coordinated function in enhancing drought tolerance by promoting dark-induced stomatal closure.
- Published
- 2017
35. Auxin-mediated Aux/IAA-ARF-HB signaling cascade regulates secondary xylem development in Populus
- Author
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Wanxiang Lu, Hong Yu, Yongli Li, Di Fan, Chaofeng Li, Keming Luo, Yun Shen, Fu He, Xiaokang Fu, Changzheng Xu, and Hua Cassan Wang
- Subjects
0106 biological sciences ,0301 basic medicine ,Physiology ,Transgene ,Plant Science ,Biology ,01 natural sciences ,03 medical and health sciences ,Auxin ,Gene Expression Regulation, Plant ,Xylem ,Vascular cambium ,Gene ,Transcription factor ,Plant Proteins ,chemistry.chemical_classification ,Indoleacetic Acids ,fungi ,food and beverages ,Promoter ,Phenotype ,Wood ,Cell biology ,030104 developmental biology ,Populus ,chemistry ,010606 plant biology & botany ,Protein Binding ,Signal Transduction - Abstract
Wood development is strictly regulated by various phytohormones and auxin plays a central regulatory role in this process. However, how the auxin signaling is transducted in developing secondary xylem during wood formation in tree species remains unclear. Here, we identified an Aux/INDOLE-3-ACETIC ACID 9 (IAA9)-AUXIN RESPONSE FACTOR 5 (ARF5) module in Populus tomentosa as a key mediator of auxin signaling to control early developing xylem development. PtoIAA9, a canonical Aux/IAA gene, is predominantly expressed in vascular cambium and developing secondary xylem and induced by exogenous auxin. Overexpression of PtoIAA9m encoding a stabilized IAA9 protein significantly represses secondary xylem development in transgenic poplar. We further showed that PtoIAA9 interacts with PtoARF5 homologs via the C-terminal III/IV domains. The truncated PtoARF5.1 protein without the III/IV domains rescued defective phenotypes caused by PtoIAA9m. Expression analysis showed that the PtoIAA9-PtoARF5 module regulated the expression of genes associated with secondary vascular development in PtoIAA9m- and PtoARF5.1-overexpressing plants. Furthermore, PtoARF5.1 could bind to the promoters of two Class III homeodomain-leucine zipper (HD-ZIP III) genes, PtoHB7 and PtoHB8, to modulate secondary xylem formation. Taken together, our results suggest that the Aux/IAA9-ARF5 module is required for auxin signaling to regulate wood formation via orchestrating the expression of HD-ZIP III transcription factors in poplar.
- Published
- 2018
36. A realistic and multilevel measurement of citywide spatial patterns of economic segregation based on human activities
- Author
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Yandong Wang, Mingxuan Dou, Xiaokang Fu, Shanmei Wu, Mengling Qiao, and Yanyan Gu
- Subjects
Alternative methods ,Sustainable development ,Index (economics) ,Sociology and Political Science ,Computer science ,05 social sciences ,0211 other engineering and technologies ,0507 social and economic geography ,021107 urban & regional planning ,02 engineering and technology ,Development ,Data science ,Term (time) ,Urban Studies ,Identification (information) ,Economic data ,Beijing ,Tourism, Leisure and Hospitality Management ,Spatial ecology ,050703 geography - Abstract
Research on the realistic and comprehensive identification of citywide spatial patterns of economic segregation is valuable for the sustainable development of cities. The consideration of human activities in segregation research inspires us to develop an alternative method to contribute to this type of research. In our method, we emphasize the combination of collective activity spaces (CASs) and spatial economic data, both of which are obtained from dynamic human activities. We first reveal the realistic use of urban spaces from human mobility patterns to generate multilevel CASs as basic analytical units. Then, we use a type of realistic economic data generated from human activities to measure the segregation level of each CAS. We realize this measurement by tailoring a segregation index, named the Term Frequency-Inverse Document Frequency-Index of Concentration at the Extremes-based (TFIDF-ICE-based) segregation index, for our economic data. Through these methods, we can uncover citywide multilevel spatial patterns of economic segregation realistically and comprehensively. Using Beijing and Wuhan as cases, we demonstrate and discuss the applicability and value of our method.
- Published
- 2021
37. The
- Author
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Fu, He, Changzheng, Xu, Xiaokang, Fu, Yun, Shen, Li, Guo, Mi, Leng, and Keming, Luo
- Subjects
MicroRNAs ,Populus ,Indoleacetic Acids ,Gene Expression Regulation, Plant ,fungi ,food and beverages ,RNA Interference ,Articles ,Plants, Genetically Modified ,Plant Roots ,Salt Stress ,Plant Proteins ,Signal Transduction - Abstract
Salt-induced developmental plasticity in a plant root system strongly depends on auxin signaling. However, the molecular events underlying this process are poorly understood. MicroRNA390 (miR390), trans-actin small interfering RNAs (tasiRNAs), and AUXIN RESPONSE FACTORs (ARFs) form a regulatory module involved in controlling lateral root (LR) growth. Here, we found that miR390 expression was strongly induced by exposure to salt during LR formation in poplar (Populus spp.) plants. miR390 overexpression stimulated LR development and increased salt tolerance, whereas miR390 knockdown caused by a short tandem target mimic repressed LR growth and compromised salt resistance. ARF3.1, ARF3.2, and ARF4 expression was inhibited significantly by the presence of salt, and transcript abundance was decreased dramatically in the miR390-overexpressing line but increased in the miR390-knockdown line. Constitutive expression of ARF4m harboring mutated trans-acting small interfering ARF-binding sites removed the salt resistance of the miR390 overexpressors. miR390 positively regulated auxin signaling in LRs subjected to salt, but ARF4 inhibited auxin signaling. Salinity stabilized the poplar Aux/IAA repressor INDOLE-3-ACETIC ACID17.1, and overexpression of an auxin/salt-resistant form of this repressor suppressed LR growth in miR390-overexpressing and ARF4-RNA interfering lines in the presence of salt. Thus, the miR390/TAS3/ARFs module is a key regulator, via modulating the auxin pathway, of LR growth in poplar subjected to salt stress.
- Published
- 2017
38. Description of a CO2 Enhanced Coal Bed Methane Field Trial Using a Multi-Lateral Horizontal Well
- Author
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Zhejun Pan, Cameron Briggs, Michael Camilleri, Luke D. Connell, Guo Benguang, Nicholas Lupton, David I. Down, John Carras, Xiaokang Fu, Meng Shangzhi, and Zhang Wenzhong
- Subjects
ECBM ,Flow (psychology) ,Management, Monitoring, Policy and Law ,Coal bed methane ,Tracer gases ,Industrial and Manufacturing Engineering ,Methane ,chemistry.chemical_compound ,Energy(all) ,TRACER ,CO2 storage ,Coal ,geography ,geography.geographical_feature_category ,Petroleum engineering ,business.industry ,Coal mining ,Pollution ,General Energy ,Inflatable ,chemistry ,Field trial ,Environmental science ,business ,Displacement (fluid) ,Water well - Abstract
Enhanced recovery of coal bed methane by CO2 injection (CO2-ECBM) offers the potential of increasing recovery of the gas in place relative to primary recovery methods while storing CO2. This paper describes a CO2-ECBM field trial that used a multi-lateral horizontal well with 2.3 km in seam length for injection. The trial, performed in China's Shanxi basin, involved transport of liquid CO2 to the injection site and pumping of this directly into the injection well. A u-tube sampling system was installed in a monitoring well 25 m from the main horizontal branch close to the vertical section of the injection well. This u-tube system comprised three intervals separated by inflatable packers from which gas and water samples were automatically collected and recovered to an on-site field laboratory for gas analysis. The middle interval of this packer assembly was positioned to collect fluid samples from the coal seam targeted for ECBM. At the start and towards the end of the period of CO2 injection, a pulse of non-adsorbing tracer gas was added to the CO2. There was clear breakthrough of the tracer in the middle packer interval of the monitoring well, demonstrating the good connection between the injection and monitoring wells. The CO2 composition of the gas sample from the coal seam gradually increased over time as injected CO2 migrated to the monitoring well and reached a maximum of 12%. Coal permeability, and thus CO2 injectivity, has been observed to decline during other CO2-ECBM field trials as higher adsorbing CO2 displaces reservoir methane. However in this trial there was no clear trend of decreasing injectivity with time, possibly due to the flow behaviour in the long horizontal well and the short periods of CO2 injection.
- Published
- 2013
39. Modeling Supply Chain Facility Location Problem and Its Solution Using a Genetic Algorithm
- Author
-
Guanglan Zhou, Xiaokang Fu, Tinggui Chen, and Bing Wang
- Subjects
Human-Computer Interaction ,Mathematical optimization ,Linear programming ,Operations research ,Artificial Intelligence ,Computer science ,Supply chain ,Genetic algorithm ,Table (database) ,Workload ,Software ,Facility location problem - Abstract
The supply chain facility location problem is an important foundation in the supply chain. The quality of facilities location directly influences the production and operation status of enterprise. Therefore, it is critical for enterprises to adopt scientific and effective methods for facility location problem assessment and a smooth decision. This article concentrates on the development status of location problem, focusing on the linear programming model and a genetic algorithm in the location problem analysis and analytical method. In the linear programming model, because the given complex table calculation method is too complicated and the workload is very large, the Excel software is proposed to solve the location problem, which can greatly improve the efficiency of enterprise facility location problem. In addition, a genetic algorithm based on MATLAB toolbox is applied to another type of facility location problem, which provides a referential method for location decision under different conditions and different facilities.
- Published
- 2014
40. Risk and decision making analyses and applications to the petroleum exploration — A certain PSC area
- Author
-
Shibin He, Xiaokang Fu, and Mingyin Zhang
- Subjects
Probability of success ,Sustainable development ,Actuarial science ,media_common.quotation_subject ,Decision tree ,Economics ,General Earth and Planetary Sciences ,Petroleum exploration ,Prudence ,General Environmental Science ,media_common - Abstract
Risk is a critical factor that an investor must take into account, regardless of where money is invested. Before making important decisions in petroleum exploration, it is standard practice to calculate the expected monetary value for each given prospect. Because of the large uncertainty inherent in decisions that involve large sums of money, the investor needs to exercise prudence. This paper describes an application of calculating the expected monetary value in a mature producing area in the Malacca Strait PSC Contract Area, Indonesia.
- Published
- 1997
41. Using Social Media to Detect Outdoor Air Pollution and Monitor Air Quality Index (AQI): A Geo-Targeted Spatiotemporal Analysis Framework with Sina Weibo (Chinese Twitter)
- Author
-
Xiaokang Fu, Yandong Wang, Ming-Hsiang Tsou, and Wei Jiang
- Subjects
China ,Big data ,Air pollution ,Decision tree ,lcsh:Medicine ,Biology ,medicine.disease_cause ,Spatio-Temporal Analysis ,Air Pollution ,medicine ,Humans ,Social media ,Cities ,lcsh:Science ,Air quality index ,Air Pollutants ,Multidisciplinary ,business.industry ,Spatiotemporal Analysis ,lcsh:R ,Data science ,Social research ,Correlation analysis ,lcsh:Q ,business ,Social Media ,Research Article ,Environmental Monitoring - Abstract
Outdoor air pollution is a serious problem in many developing countries today. This study focuses on monitoring the dynamic changes of air quality effectively in large cities by analyzing the spatiotemporal trends in geo-targeted social media messages with comprehensive big data filtering procedures. We introduce a new social media analytic framework to (1) investigate the relationship between air pollution topics posted in Sina Weibo (Chinese Twitter) and the daily Air Quality Index (AQI) published by China's Ministry of Environmental Protection; and (2) monitor the dynamics of air quality index by using social media messages. Correlation analysis was used to compare the connections between discussion trends in social media messages and the temporal changes in the AQI during 2012. We categorized relevant messages into three types, retweets, mobile app messages, and original individual messages finding that original individual messages had the highest correlation to the Air Quality Index. Based on this correlation analysis, individual messages were used to monitor the AQI in 2013. Our study indicates that the filtered social media messages are strongly correlated to the AQI and can be used to monitor the air quality dynamics to some extent.
- Published
- 2015
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