27 results on '"Mengyao Feng"'
Search Results
2. Salmonellosis outbreak archive in China: data collection and assembly
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Zining Wang, Chenghu Huang, Yuhao Liu, Jiaqi Chen, Rui Yin, Chenghao Jia, Xiamei Kang, Xiao Zhou, Sihao Liao, Xiuyan Jin, Mengyao Feng, Zhijie Jiang, Yan Song, Haiyang Zhou, Yicheng Yao, Lin Teng, Baikui Wang, Yan Li, and Min Yue
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Science - Abstract
Abstract Infectious disease outbreaks transcend the medical and public health realms, triggering widespread panic and impeding socio-economic development. Considering that self-limiting diarrhoea of sporadic cases is usually underreported, the Salmonella outbreak (SO) study offers a unique opportunity for source tracing, spatiotemporal correlation, and outbreak prediction. To summarize the pattern of SO and estimate observational epidemiological indicators, 1,134 qualitative reports screened from 1949 to 2023 were included in the systematic review dataset, which contained a 506-study meta-analysis dataset. In addition to the dataset comprising over 50 columns with a total of 46,494 entries eligible for inclusion in systematic reviews or input into prediction models, we also provide initial literature collection datasets and datasets containing socio-economic and climate information for relevant regions. This study has a broad impact on advancing knowledge regarding epidemic trends and prevention priorities in diverse salmonellosis outbreaks and guiding rational policy-making or predictive modeling to mitigate the infringement upon the right to life imposed by significant epidemics.
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- 2024
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3. An integrated nationwide genomics study reveals transmission modes of typhoid fever in China
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Ye Feng, Hang Pan, Beiwen Zheng, Fang Li, Lin Teng, Zhijie Jiang, Mengyao Feng, Xiao Zhou, Xianqi Peng, Xuebin Xu, Haoqiu Wang, Beibei Wu, Yonghong Xiao, Stephen Baker, Guoping Zhao, and Min Yue
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Salmonella Typhi ,typhoidal fever ,transmission ,exploiting genomics ,pandemic clone ,Microbiology ,QR1-502 - Abstract
ABSTRACT Typhoid fever, caused by Salmonella Typhi (S. Typhi), is a life-threatening disease, usually food-borne and commonly associated with international travel. The disease transmission remains endemic in many low- and middle-income countries, representing further hotspots for seeding new global outbreaks. China has historically been affected by typhoid fever, but the respective roles of local transmission and importation remain unknown. Here, we generated a nationwide map of the typhoid burden in China and investigated the associations between typhoid disease, climate and various socioeconomic parameters. To assess transmission dynamics, we sub-sampled S. Typhi isolated within China over five decades and sequenced their genomes. The resulting 705 new genomes, placed in context with 5,190 global isolates from 87 countries on six continents, led to the discovery of several predominant inland Chinese clones belonging to the clades 2.1/2.3/3.2/4.3. These clones were associated with multiple introductions from overseas, followed by local expansion. Notably, 4.3.1 isolates from eastern China were not genetically close to those from northwestern China but to the international isolates, indicating their association with international travel. Additional in vitro assays showed that 4.3.1 elaborated better intracellular survival, acid tolerance, and desiccation tolerance than other lineages, partially explaining its success. For the first time, we have probed typhoid transmission in China, finding local transmission and importation, which could guide the policy for typhoid control. IMPORTANCE Typhoid fever is a life-threatening disease caused by Salmonella enterica serovar Typhi, resulting in a significant disease burden across developing countries. Historically, China was very much close to the global epicenter of typhoid, but the role of typhoid transmission within China and among epicenter remains overlooked in previous investigations. By using newly produced genomics on a national scale, we clarify the complex local and global transmission history of such a notorious disease agent in China spanning the most recent five decades, which largely undermines the global public health network.
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- 2023
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4. Generative pretraining from large-scale transcriptomes for single-cell deciphering
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Hongru Shen, Jilei Liu, Jiani Hu, Xilin Shen, Chao Zhang, Dan Wu, Mengyao Feng, Meng Yang, Yang Li, Yichen Yang, Wei Wang, Qiang Zhang, Jilong Yang, Kexin Chen, and Xiangchun Li
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Automation in bioinformatics ,Data processing in systems biology ,Transcriptomics ,Science - Abstract
Summary: Exponential accumulation of single-cell transcriptomes poses great challenge for efficient assimilation. Here, we present an approach entitled generative pretraining from transcriptomes (tGPT) for learning feature representation of transcriptomes. tGPT is conceptually simple in that it autoregressive models the ranking of a gene in the context of its preceding neighbors. We developed tGPT with 22.3 million single-cell transcriptomes and used four single-cell datasets to evalutate its performance on single-cell analysis tasks. In addition, we examine its applications on bulk tissues. The single-cell clusters and cell lineage trajectories derived from tGPT are highly aligned with known cell labels and states. The feature patterns of tumor bulk tissues learned by tGPT are associated with a wide range of genomic alteration events, prognosis, and treatment outcome of immunotherapy. tGPT represents a new analytical paradigm for integrating and deciphering massive amounts of transcriptome data and it will facilitate the interpretation and clinical translation of single-cell transcriptomes.
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- 2023
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- View/download PDF
5. Change in antimicrobial susceptibility of Listeria spp. in response to stress conditions
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Haoqiu Wang, Mengyao Feng, Tanveer Muhammad Anwar, Wenqin Chai, Abdelaziz Ed-Dra, Xiamei Kang, Kalliopi Rantsiou, Corinna Kehrenberg, Min Yue, and Yan Li
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Listeria monocytogenes ,Listeria ivanovii ,Listeria innocua ,food processing environment ,stress resistance ,antimicrobial resistance ,Nutrition. Foods and food supply ,TX341-641 ,Food processing and manufacture ,TP368-456 - Abstract
Listeria species are exposed to various stressors throughout the food chain, which are crucial for microbe mitigation strategy in the food industry. However, the survival capabilities and development of antimicrobial resistance by Listeria spp. under different food processing environments (FPEs) stressors are not yet well understood. Hence, this study aims to determine the difference in survivability and antimicrobial susceptibility of L. monocytogenes (Lm) and other Listeria species (non-Lm) strains exposed to different FPEs stressors, including heat, acidic and alkaline pH, UV irradiation, and osmotic stress. For this, a collection of 11 Lm and 10 non-Lm strains were used to conduct experiments. This study showed that Lm strains were relatively more tolerant to environmental stresses than non-Lm strains (p > 0.05). Additionally, the evaluation of stress-induced resistance toward antimicrobials showed that anaerobic incubation, after exposition to environmental stresses, rendered Lm and non-Lm more resistant to antimicrobial agents than aerobic incubation. Furthermore, the study observed that different stressors induced an increase in minimum inhibitory concentrations (MICs) of certain antimicrobials. Specifically, heat stress persuaded an increase in MICs of tetracycline under aerobic incubation, and gentamicin and ciprofloxacin under anaerobic incubation. Acidic/alkaline pH induced an increase in MICs of gentamicin, ciprofloxacin, and trimethoprim-sulfamethoxazole, especially under anaerobic incubation. However, UV stress induced increase in MICs of tetracycline and trimethoprim-sulfamethoxazole under aerobic incubation and gentamicin, ciprofloxacin, and trimethoprim-sulfamethoxazole under anaerobic incubation. Additionally, osmotic stress induced an increase in MICs of tetracycline and ampicillin under aerobic incubation and gentamicin, tetracycline, and trimethoprim-sulfamethoxazole under anaerobic incubation. Collectively, this study highlights that stress tolerance may contribute to the predominance of Listeria species among FPEs and induce the development of antimicrobial resistance even without antibiotic selection pressure. The findings of this study may guide updated strategies to mitigate Listeria species in the food industry.
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- 2023
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6. Prediction of Two Molecular Subtypes of Gastric Cancer Based on Immune Signature
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Dan Wu, Mengyao Feng, Hongru Shen, Xilin Shen, Jiani Hu, Jilei Liu, Yichen Yang, Yang Li, Meng Yang, Wei Wang, Qiang Zhang, Fangfang Song, Ben Liu, Kexin Chen, and Xiangchun Li
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gastric cancer ,immune signature ,molecular subtypes ,prognosis ,computational biology ,Genetics ,QH426-470 - Abstract
Gastric cancer is the fifth most common type of human cancer and the third leading cause of cancer-related death. The purpose of this study is to investigate the immune infiltration signatures of gastric cancer and their relation to prognosis. We identified two distinct subtypes of gastric cancer (C1/C2) characterized by different immune infiltration signatures. C1 is featured by immune resting, epithelial–mesenchymal transition, and angiogenesis pathways, while C2 is featured by enrichment of the MYC target, oxidative phosphorylation, and E2F target pathways. The C2 subtype has a better prognosis than the C1 subtype (HR = 0.61, 95% CI: 0.44–0.85; log-rank test, p = 0.0029). The association of C1/C2 with prognosis remained statistically significant (HR = 0.62, 95% CI: 0.44–0.87; p = 0.006) after controlling for age, gender, and stage. The prognosis prediction of C1/C2 was verified in four independent cohorts (including an internal cohort). In summary, our study is helpful for better understanding of the association between immune infiltration and the prognosis of gastric cancer.
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- 2022
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7. Miscell: An efficient self-supervised learning approach for dissecting single-cell transcriptome
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Hongru Shen, Yang Li, Mengyao Feng, Xilin Shen, Dan Wu, Chao Zhang, Yichen Yang, Meng Yang, Jiani Hu, Jilei Liu, Wei Wang, Qiang Zhang, Fangfang Song, Jilong Yang, Kexin Chen, and Xiangchun Li
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Biological sciences ,Neural networks ,Transcriptomics ,Science - Abstract
Summary: We developed Miscell, a self-supervised learning approach with deep neural network as latent feature encoder for mining information from single-cell transcriptomes. We demonstrated the capability of Miscell with canonical single-cell analysis tasks including delineation of single-cell clusters and identification of cluster-specific marker genes. We evaluated Miscell along with three state-of-the-art methods on three heterogeneous datasets. Miscell achieved at least comparable or better performance than the other methods by significant margin on a variety of clustering metrics such as adjusted rand index, normalized mutual information, and V-measure score. Miscell can identify cell-type specific markers by quantifying the influence of genes on cell clusters via deep learning approach.
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- 2021
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8. Transcriptomic Analysis Identified Two Subtypes of Brain Tumor Characterized by Distinct Immune Infiltration and Prognosis
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Xilin Shen, Xiaoli Wang, Hongru Shen, Mengyao Feng, Dan Wu, Yichen Yang, Yang Li, Meng Yang, Wei Ji, Wei Wang, Qiang Zhang, Fangfang Song, Ben Liu, Kexin Chen, and Xiangchun Li
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brain tumor ,immune infiltration ,prognosticator ,transcriptome ,molecular subtype ,Neoplasms. Tumors. Oncology. Including cancer and carcinogens ,RC254-282 - Abstract
BackgroundBrain tumor ranks as the most devastating cancer type. The complex tumor immune microenvironment prevents brain tumor from receiving therapeutic benefits. The purpose of this study was to stratify brain tumors based on their distinct immune infiltration signatures to facilitate better clinical decision making and prognosis prediction.MethodsWe developed a deep learning model to characterize immune infiltration from transcriptome. The developed model was applied to distill expression signatures of transcriptome of brain tumor samples. We performed molecular subtyping with the extracted expression signatures to unveil brain tumor subtypes. Computational methods, including gene set enrichment analysis, Kaplan-Meier survival and multivariate Cox regression analyses, were employed.ResultsWe identified two distinctive subtypes (i.e. C1/2) of brain tumor featured by distinct immune infiltration signatures. The C1 subtype is characterized by protective immune infiltration signatures, including high infiltration of CD8+ T cells and activation of CX3CL1. The C2 subtype has an extensive infiltration of tumor-associated macrophages and microglia, and was enriched with immune suppressive, wound-healing, and angiogenic signatures. The C1 subtype had significantly better prognosis as compared with C2 (Log-rank test, HR: 2.5, 95% CI: 2.2 – 2.7; P = 8.2e-78). This difference remained statistically significant (multivariate Cox model, HR: 2.2, 95% CI: 1.7 – 2.9; P = 3.7e-10) by taking into account age, gender, recurrent/secondary status at sampling time, tumor grade, histology, radio-chemotherapy, IDH mutation, MGMT methylation, and co-deletion of 1p and 19q. This finding was validated in six datasets. The C2 subtype of glioblastoma patients with IDH mutation has poor survival analogous to those without IDH mutation (Log-rank test, adjusted P = 0.8), while C1 has favorable prognosis as compared with glioblastoma of C2 subtype with IDH mutation (Log-rank test, adjusted P = 1.2e-3) or without IDH mutation (Log-rank test, adjusted P = 1.3e-6).ConclusionsWe identified two distinctive subtypes of brain tumor with different immune infiltration signatures, which might be helpful as an independent prognosticator for brain tumor.
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- 2021
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9. Prevalence and Genomic Investigation of Multidrug-Resistant Salmonella Isolates from Companion Animals in Hangzhou, China
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Lin Teng, Sihao Liao, Xin Zhou, Chenghao Jia, Mengyao Feng, Hang Pan, Zhengxin Ma, and Min Yue
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Salmonella ,pets ,prevalence ,antimicrobial resistance ,whole genome sequencing ,Therapeutics. Pharmacology ,RM1-950 - Abstract
Salmonella is a group of bacteria that constitutes the leading cause of diarrheal diseases, posing a great disease burden worldwide. There are numerous pathways for zoonotic Salmonella transmission to humans; however, the role of companion animals in spreading these bacteria is largely underestimated in China. We aimed to investigate the prevalence of Salmonella in pet dogs and cats in Hangzhou, China, and characterize the antimicrobial resistance profile and genetic features of these pet-derived pathogens. In total, 137 fecal samples of pets were collected from an animal hospital in Hangzhou in 2018. The prevalence of Salmonella was 5.8% (8/137) in pets, with 9.3% (5/54) of cats and 3.6% (3/83) of dogs being Salmonella positive. By whole-genome sequencing (WGS), in silico serotyping, and multilocus sequence typing (MLST), 26 pet-derived Salmonella isolates were identified as Salmonella Dublin (ST10, n = 22) and Salmonella Typhimurium (ST19, n = 4). All of the isolates were identified as being multidrug-resistant (MDR), by conducting antimicrobial susceptibility testing under both aerobic and anaerobic conditions. The antibiotics of the most prevalent resistance were streptomycin (100%), cotrimoxazole (100%), tetracycline (96.20%), and ceftriaxone (92.30%). Versatile antimicrobial-resistant genes were identified, including floR (phenicol-resistant gene), blaCTX-M-15, and blaCTX-M-55 (extended-spectrum beta-lactamase genes). A total of 11 incompatible (Inc) plasmids were identified, with IncA/C2, IncFII(S), and IncX1 being the most predominant among Salmonella Dublin, and IncFIB(S), IncFII(S), IncI1, and IncQ1 being the most prevailing among Salmonella Typhimurium. Our study applied WGS to characterize pet-derived Salmonella in China, showing the presence of MDR Salmonella in pet dogs and cats with a high diversity of ARGs and plasmids. These data indicate a necessity for the regular surveillance of pet-derived pathogens to mitigate zoonotic diseases.
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- 2022
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10. An immunomodulatory signature of responsiveness to immune checkpoint blockade therapy
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Hongru Shen, Xilin Shen, Dan Wu, Mengyao Feng, Yichen Yang, Yang Li, Meng Yang, Wei Wang, Qiang Zhang, Fangfang Song, Kexin Chen, and Xiangchun Li
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Medicine (General) ,R5-920 - Published
- 2020
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11. Learning a Convolutional Autoencoder for Nighttime Image Dehazing
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Mengyao Feng, Teng Yu, Mingtao Jing, and Guowei Yang
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nighttime haze ,color correction ,guide filtering ,autoencoder network ,Information technology ,T58.5-58.64 - Abstract
Currently, haze removal of images captured at night for foggy scenes rely on the traditional, prior-based methods, but these methods are frequently ineffective at dealing with night hazy images. In addition, the light sources at night are complicated and there is a problem of inconsistent brightness. This makes the estimation of the transmission map complicated in the night scene. Based on the above analysis, we propose an autoencoder method to solve the problem of overestimation or underestimation of transmission captured by the traditional, prior-based methods. For nighttime hazy images, we first remove the color effect of the haze image with an edge-preserving maximum reflectance prior (MRP) method. Then, the hazy image without color influence is input into the self-encoder network with skip connections to obtain the transmission map. Moreover, instead of using the local maximum method, we estimate the ambient illumination through a guiding image filtering. In order to highlight the effectiveness of our experiments, a large number of comparison experiments were conducted between our method and the state-of-the-art methods. The results show that our method can effectively suppress the halo effect and reduce the effectiveness of glow. In the experimental part, we calculate that the average Peak Signal to Noise Ratio (PSNR) is 21.0968 and the average Structural Similarity (SSIM) is 0.6802.
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- 2020
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12. Scalable batch-correction approach for integrating large-scale single-cell transcriptomes.
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Xilin Shen, Hongru Shen, Dan Wu, Mengyao Feng, Jiani Hu, Jilei Liu, Yichen Yang 0004, Meng Yang, Yang Li, Lei Shi, Kexin Chen, and Xiangchun Li
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- 2022
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13. A universal approach for integrating super large-scale single-cell transcriptomes by exploring gene rankings.
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Hongru Shen, Xilin Shen, Mengyao Feng, Dan Wu, Chao Zhang, Yichen Yang 0004, Meng Yang, Jiani Hu, Jilei Liu, Wei Wang, Yang Li, Qiang Zhang, Jilong Yang, Kexin Chen, and Xiangchun Li
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- 2022
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14. One-Dimensional Heterobimetallic Au/Ag Coordination Polymer Showing a Selective, Reversible, and Visible Vapor-Chromic Photoluminescent Response toward Methanol
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Mengyao Feng, Fuyuan Liu, Ningwen Yang, Jiayao Yu, Wei Yang, David James Young, Xiang-Qian Cao, Hong-Xi Li, and Zhi-Gang Ren
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Inorganic Chemistry ,Physical and Theoretical Chemistry - Published
- 2023
15. A Cross-Sectional Study of Companion Animal-Derived Multidrug-Resistant Escherichia coli in Hangzhou, China
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Lin Teng, Mengyao Feng, Sihao Liao, Zhijie Zheng, Chenghao Jia, Xin Zhou, Reshma B. Nambiar, Zhengxin Ma, and Min Yue
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Microbiology (medical) ,Infectious Diseases ,General Immunology and Microbiology ,Ecology ,Physiology ,Genetics ,Cell Biology - Abstract
MDR Escherichia coli are considered a global threat because of the decreasing options for antimicrobial therapy. Companion animals could be a reservoir of MDR E. coli , and the numbers of pets and households owning pets in China are booming.
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- 2023
16. Experimental Study on Damage Evolution of Soft-Hard Interactive Rock Based on Improved Transformer Algorithm
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xianyin, Qi, primary, Xu, Mingzhe, additional, mengyao, Feng, additional, and diandong, Geng, additional
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- 2023
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17. Infant food production environments: A potential reservoir for vancomycin-resistant enterococci non-nosocomial infections
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Zining Wang, Sihao Liao, Guanwen Huang, Mengyao Feng, Rui Yin, Lin Teng, Chenghao Jia, Yicheng Yao, Min Yue, and Yan Li
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General Medicine ,Microbiology ,Food Science - Published
- 2023
18. Generative pretraining from large-scale transcriptomes: Implications for single-cell deciphering and clinical translation
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Hongru Shen, Xilin Shen, Jiani Hu, Jilei Liu, Chao Zhang, Dan Wu, Mengyao Feng, Meng Yang, Yang Li, Yichen Yang, Wei Wang, Qiang Zhang, Jilong Yang, Kexin Chen, and Xiangchun Li
- Abstract
Exponential accumulation of single-cell transcriptomes poses great challenge for efficient assimilation. Here, we present an approach entitled tGPT towards integration of 22.3 million single-cell transcriptomes by modeling gene expression rankings as generative pretraining task. tGPT is conceptually simple in that it autoregressively models the ranking of a gene in the context of its preceding neighbors. We demonstrated the high performance of tGPT on a range of fundamental single-cell analysis tasks and novel applications on bulk tissues. The single-cell clusters and cell lineage trajectories derived from tGPT are highly aligned with known cell labels and states. The feature patterns of tumor bulk tissues learned by tGPT are associated with a wide range of genomic alteration events, prognosis and treatment outcome of immunotherapy. tGPT represents a new analytical paradigm for integrating and deciphering massive amount of transcriptome data and it will facilitate the interpretation and clinical translation of single-cell transcriptomes.
- Published
- 2022
19. A universal approach for integrating super large-scale single-cell transcriptomes by exploring gene rankings
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Chao Zhang, Jilong Yang, Xiangchun Li, Yichen Yang, Mengyao Feng, Xilin Shen, Wei Wang, Yang Li, Hongru Shen, Jilei Liu, Jiani Hu, Dan Wu, Meng Yang, Qiang Zhang, and Kexin Chen
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Cell specific ,Computer science ,Scale (chemistry) ,Computational biology ,Expression (mathematics) ,Transcriptome ,Mice ,Identification (information) ,Expression data ,Exome Sequencing ,Animals ,Cluster Analysis ,Gene Regulatory Networks ,Single-Cell Analysis ,Cluster analysis ,Gene ,Molecular Biology ,Information Systems - Abstract
Advancement in single-cell RNA sequencing leads to exponential accumulation of single-cell expression data. However, there is still lack of tools that could integrate these unlimited accumulation of single-cell expression data. Here, we presented a universal approach iSEEEK for integrating super large-scale single-cell expression via exploring expression rankings of top-expressing genes. We developed iSEEEK with 13.7 million single-cells. We demonstrated the efficiency of iSEEEK with canonical single-cell downstream tasks on five heterogenous datasets encompassing human and mouse samples. iSEEEK achieved good clustering performance benchmarked against well-annotated cell labels. In addition, iSEEEK could transfer its knowledge learned from large-scale expression data on new dataset that was not involved in its development. iSEEEK enables identification of gene-gene interaction networks that are characteristic of specific cell types. Our study presents a simple and yet effective method to integrate super large-scale single-cell transcriptomes and would facilitate translational single-cell research from bench to bedside.
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- 2022
20. Scalable Batch-Correction Method for Integrating Large-Scale Single-Cell Transcriptomes
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Xilin Shen, Hongru Shen, Dan Wu, Mengyao Feng, Jiani Hu, Jilei Liu, Yichen Yang, Meng Yang, Yang Li, Lei Shi, Kexin Chen, and Xiangchun Li
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- 2022
21. Transcriptomic Analysis Identified Two Subtypes of Brain Tumor Characterized by Distinct Immune Infiltration and Prognosis
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Fangfang Song, Yang Li, Ben Liu, Dan Wu, Hongru Shen, Xilin Shen, Kexin Chen, Mengyao Feng, Qiang Zhang, Xiaoli Wang, Meng Yang, Wei Ji, Wei Wang, Yichen Yang, and Xiangchun Li
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Cancer Research ,Proportional hazards model ,immune infiltration ,Brain tumor ,Neoplasms. Tumors. Oncology. Including cancer and carcinogens ,Biology ,medicine.disease ,molecular subtype ,Subtyping ,Transcriptome ,Immune system ,Oncology ,prognosticator ,medicine ,Cancer research ,CX3CL1 ,Infiltration (medical) ,transcriptome ,CD8 ,brain tumor ,RC254-282 ,Original Research - Abstract
BackgroundBrain tumor ranks as the most devastating cancer type. The complex tumor immune microenvironment prevents brain tumor from receiving therapeutic benefits. The purpose of this study was to stratify brain tumors based on their distinct immune infiltration signatures to facilitate better clinical decision making and prognosis prediction.MethodsWe developed a deep learning model to characterize immune infiltration from transcriptome. The developed model was applied to distill expression signatures of transcriptome of brain tumor samples. We performed molecular subtyping with the extracted expression signatures to unveil brain tumor subtypes. Computational methods, including gene set enrichment analysis, Kaplan-Meier survival and multivariate Cox regression analyses, were employed.ResultsWe identified two distinctive subtypes (i.e. C1/2) of brain tumor featured by distinct immune infiltration signatures. The C1 subtype is characterized by protective immune infiltration signatures, including high infiltration of CD8+ T cells and activation of CX3CL1. The C2 subtype has an extensive infiltration of tumor-associated macrophages and microglia, and was enriched with immune suppressive, wound-healing, and angiogenic signatures. The C1 subtype had significantly better prognosis as compared with C2 (Log-rank test, HR: 2.5, 95% CI: 2.2 – 2.7; P = 8.2e-78). This difference remained statistically significant (multivariate Cox model, HR: 2.2, 95% CI: 1.7 – 2.9; P = 3.7e-10) by taking into account age, gender, recurrent/secondary status at sampling time, tumor grade, histology, radio-chemotherapy, IDH mutation, MGMT methylation, and co-deletion of 1p and 19q. This finding was validated in six datasets. The C2 subtype of glioblastoma patients with IDH mutation has poor survival analogous to those without IDH mutation (Log-rank test, adjusted P = 0.8), while C1 has favorable prognosis as compared with glioblastoma of C2 subtype with IDH mutation (Log-rank test, adjusted P = 1.2e-3) or without IDH mutation (Log-rank test, adjusted P = 1.3e-6).ConclusionsWe identified two distinctive subtypes of brain tumor with different immune infiltration signatures, which might be helpful as an independent prognosticator for brain tumor.
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- 2021
22. An immunomodulatory signature of responsiveness to immune checkpoint blockade therapy
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Dan Wu, Fangfang Song, Kexin Chen, Hongru Shen, Xiangchun Li, Wei Wang, Qiang Zhang, Yichen Yang, Xilin Shen, Mengyao Feng, Yang Li, and Meng Yang
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Medicine (General) ,R5-920 ,business.industry ,Cancer research ,Molecular Medicine ,Medicine (miscellaneous) ,Medicine ,business ,Letter to Editor ,Immune checkpoint ,Signature (logic) ,Blockade - Published
- 2020
23. Learning a Convolutional Autoencoder for Nighttime Image Dehazing
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Mingtao Jing, Mengyao Feng, Teng Yu, and Guowei Yang
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autoencoder network ,Brightness ,Haze ,lcsh:T58.5-58.64 ,business.industry ,Computer science ,lcsh:Information technology ,Color correction ,Color effect ,020207 software engineering ,02 engineering and technology ,guide filtering ,Autoencoder ,Peak signal-to-noise ratio ,Image (mathematics) ,Transmission (telecommunications) ,color correction ,0202 electrical engineering, electronic engineering, information engineering ,020201 artificial intelligence & image processing ,Computer vision ,Artificial intelligence ,business ,Information Systems ,nighttime haze - Abstract
Currently, haze removal of images captured at night for foggy scenes rely on the traditional, prior-based methods, but these methods are frequently ineffective at dealing with night hazy images. In addition, the light sources at night are complicated and there is a problem of inconsistent brightness. This makes the estimation of the transmission map complicated in the night scene. Based on the above analysis, we propose an autoencoder method to solve the problem of overestimation or underestimation of transmission captured by the traditional, prior-based methods. For nighttime hazy images, we first remove the color effect of the haze image with an edge-preserving maximum reflectance prior (MRP) method. Then, the hazy image without color influence is input into the self-encoder network with skip connections to obtain the transmission map. Moreover, instead of using the local maximum method, we estimate the ambient illumination through a guiding image filtering. In order to highlight the effectiveness of our experiments, a large number of comparison experiments were conducted between our method and the state-of-the-art methods. The results show that our method can effectively suppress the halo effect and reduce the effectiveness of glow. In the experimental part, we calculate that the average Peak Signal to Noise Ratio (PSNR) is 21.0968 and the average Structural Similarity (SSIM) is 0.6802.
- Published
- 2020
- Full Text
- View/download PDF
24. Miscell: An efficient self-supervised learning approach for dissecting single-cell transcriptome
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Chao Zhang, Xilin Shen, Jilong Yang, Yang Li, Qiang Zhang, Wei Wang, Jiani Hu, Jilei Liu, Dan Wu, Kexin Chen, Xiangchun Li, Fangfang Song, Meng Yang, Yichen Yang, Hongru Shen, and Mengyao Feng
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Multidisciplinary ,Artificial neural network ,business.industry ,Computer science ,Science ,Deep learning ,Rand index ,Pattern recognition ,Article ,Biological sciences ,Identification (information) ,Margin (machine learning) ,Feature (machine learning) ,Artificial intelligence ,Transcriptomics ,Cluster analysis ,business ,Encoder ,Neural networks - Abstract
Summary We developed Miscell, a self-supervised learning approach with deep neural network as latent feature encoder for mining information from single-cell transcriptomes. We demonstrated the capability of Miscell with canonical single-cell analysis tasks including delineation of single-cell clusters and identification of cluster-specific marker genes. We evaluated Miscell along with three state-of-the-art methods on three heterogeneous datasets. Miscell achieved at least comparable or better performance than the other methods by significant margin on a variety of clustering metrics such as adjusted rand index, normalized mutual information, and V-measure score. Miscell can identify cell-type specific markers by quantifying the influence of genes on cell clusters via deep learning approach., Graphical abstract, Highlights • We presented a deep learning approach Miscell to dissecting single-cell transcriptomes • Miscell achieved high performance on canonical single-cell analysis tasks • Miscell can transfer knowledge learned from single-cell transcriptomes to bulk tumors, Biological sciences; Neural networks; Transcriptomics
- Published
- 2021
25. One-step hydrothermal synthesis of cobalt and potassium codoped CdSe quantum dots with high visible light photocatalytic activity
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Weidong Shi, Mingjun Zhou, Yongsheng Yan, Changchang Ma, Pengwei Huo, Wu Dan, Mengyao Feng, Xinlin Liu, and Zhongfei Ma
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Materials science ,Diffuse reflectance infrared fourier transform ,Quantum dot ,Photocatalysis ,Hydrothermal synthesis ,General Materials Science ,General Chemistry ,Electronic structure ,Condensed Matter Physics ,Photodegradation ,Photochemistry ,High-resolution transmission electron microscopy ,Fluorescence spectroscopy - Abstract
The effect of metal ion doping on the electronic structure and optical properties of CdSe quantum dots has been investigated by various characterization techniques and experiments. Various cation codoped CdSe quantum dot photocatalysts were synthesized via a hydrothermal method. The prepared quantum dots were examined using X-ray diffraction, fluorescence spectroscopy, X-ray photoelectron spectroscopy, high resolution transmission electron microscopy, and UV–vis diffuse reflectance spectroscopy. The activities of the photocatalysts were evaluated with respect to the photodegradation of tetracycline hydrochloride solutions under simulated sunlight irradiation. 3%Co–4%K/CdSe quantum dots showed a higher photocatalytic activity than others within 30 min of visible light irradiation. Furthermore, there was hardly any decrease in the catalytic efficiency after the fourth experimental cycle. Identification data illustrate that Co and K codoping may cause improvement in the photocatalytic performance of CdSe quantum dots, which is crucial for tetracycline hydrochloride degradation under simulated sunlight irradiation. Therefore, this study demonstrates a promising strategy for the design of highly efficient photocatalysts for the remediation of aqueous pollutants.
- Published
- 2015
26. Metal ion doped CdSe quantum dots prepared by hydrothermal synthesis: enhanced photocatalytic activity and stability under visible light
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Changchang Ma, Weidong Shi, Mengyao Feng, Jianming Pan, Mingjun Zhou, Wu Yuting, Yongsheng Yan, Xinlin Liu, and Pengwei Huo
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Materials science ,Absorption spectroscopy ,Metal ions in aqueous solution ,Inorganic chemistry ,Doping ,Ocean Engineering ,Photochemistry ,Pollution ,X-ray photoelectron spectroscopy ,Quantum dot ,Photocatalysis ,Hydrothermal synthesis ,Water Science and Technology ,Visible spectrum - Abstract
Different kind of metal ion doped CdSe quantum dots (QDs) are synthesized by a simple hydrothermal method. The prepared samples are characterized by powder X-ray diffraction, transmission electron microscopy, UV-vis absorption spectra, and X-ray photoelectron spectra (XPS), while the catalytic activities of photocatalysts are tested by photocatalytic degradation of tetracycline hydrochloride under visible-light irradiation. The results show that the 4 mol% Co-doped CdSe QDs exhibit the best photocatalytic activities under visible-light irradiation. While the solution condition is changed to further evaluate their photocatalytic activities, it can be concluded that the existence of cationic surfactant gives the best result and the degradation efficiency is 85.47%. Moreover, there is almost no loss of photocatalytic activities after four cycles. Experimentally and theoretically, this study shows that the method of metal ions doping will be useful for the improvement of photocatalytic activities and ...
- Published
- 2014
27. Protein tyrosine phosphatase Meg2 dephosphorylates signal transducer and activator of transcription 3 and suppresses tumor growth in breast cancer
- Author
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Yanfang Ju, Kun Meng, Yi Li, Zhizhuang Joe Zhao, Fangli Ren, Mengyao Feng, Zhijie Chang, Yinyin Wang, Yangmeng Wang, Yongtao Geng, Fuqin Su, and Yu Rong
- Subjects
STAT3 Transcription Factor ,Phosphatase ,Molecular Sequence Data ,Mice, Nude ,Breast Neoplasms ,Protein tyrosine phosphatase ,macromolecular substances ,Biology ,Dephosphorylation ,Gene Knockout Techniques ,Mice ,Cell Line, Tumor ,Animals ,Humans ,Tyrosine ,Phosphorylation ,STAT3 ,Cell Proliferation ,Medicine(all) ,Mice, Inbred BALB C ,Base Sequence ,Protein Tyrosine Phosphatases, Non-Receptor ,Xenograft Model Antitumor Assays ,STAT protein ,Cancer research ,biology.protein ,Female ,Research Article ,Signal Transduction - Abstract
Introduction Signal transducer and activator of transcription 3 (STAT3) is over-activated or phosphorylated in breast cancers. The hyper-phosphorylation of STAT3 was attributed to either up-regulated phosphorylation by several tyrosine-kinases or down-regulated activity of phosphatases. Although several factors have been identified to phosphorylate STAT3, it remains unclear how STAT3 is dephosphorylated by PTPMeg2. The aim of this study was to determine the role of PTPMeg2 as a phosphatase in regulation of the activity of STAT3 in breast cancers. Methods Immunoprecipitation assays were used to study the interaction of STAT3 with PTPMeg2. A series of biochemistry experiments were performed to evaluate the role of PTPMeg2 in the dephosphorylation of STAT3. Two breast cancer cell lines MCF7 (PTPMeg2 was depleted as it was endogenously high) and MDA-MB-231 (PTPMeg2 was overexpressed as it was endogenously low) were used to compare the level of phosphorylated STAT3 and the tumor growth ability in vitro and in vivo. Samples from breast carcinoma (n = 73) were subjected to a pair-wise Pearson correlation analysis for the correlation of levels of PTPMeg2 and phosphorylated STAT3. Results PTPMeg2 directly interacts with STAT3 and mediates its dephosphorylation in the cytoplasm. Over-expression of PTPMeg2 decreased tyrosine phosphorylation of STAT3 while depletion of PTPMeg2 increased its phosphorylation. The decreased tyrosine phosphorylation of STAT3 is coupled with suppression of STAT3 transcriptional activity and reduced tumor growth in vitro and in vivo. Levels of PTPMeg2 and phosphorylated STAT3 were inversely correlated in breast cancer tissues (P = 0.004). Conclusions PTPMeg2 is an important phosphatase for the dephosphorylation of STAT3 and plays a critical role in breast cancer development.
- Published
- 2012
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