130 Works

Additional file 12 of Decoding the colorectal cancer ecosystem emphasizes the cooperative role of cancer cells, TAMs and CAFsin tumor progression

Rongfang Shen, Ping Li, Botao Zhang, Lin Feng & Shujun Cheng
Additional file 12: Figure S5. Characterization of myeloid cells in the KUL3 cohort. A. UMAP plot of myeloid cells colored by cell cluster and sample origin. B. Heatmap of marker genes identified through Seurat. For each cell cluster, cells were down-sampled to 100. C. Heatmap plot of the top 5 ranked regulons in TAM1-TAM4 identified by pySCENIC. D. Dot plot of the correlation between the proportions of C4 cells in epithelial cells and macrophages (left),...

Additional file 12 of Decoding the colorectal cancer ecosystem emphasizes the cooperative role of cancer cells, TAMs and CAFsin tumor progression

Rongfang Shen, Ping Li, Botao Zhang, Lin Feng & Shujun Cheng
Additional file 12: Figure S5. Characterization of myeloid cells in the KUL3 cohort. A. UMAP plot of myeloid cells colored by cell cluster and sample origin. B. Heatmap of marker genes identified through Seurat. For each cell cluster, cells were down-sampled to 100. C. Heatmap plot of the top 5 ranked regulons in TAM1-TAM4 identified by pySCENIC. D. Dot plot of the correlation between the proportions of C4 cells in epithelial cells and macrophages (left),...

Additional file 15 of Decoding the colorectal cancer ecosystem emphasizes the cooperative role of cancer cells, TAMs and CAFsin tumor progression

Rongfang Shen, Ping Li, Botao Zhang, Lin Feng & Shujun Cheng
Additional file 15: Figure S8. Workflow of this study. Single-cell transcriptomes and bulk RNA-seq data were integrated to fully analyze the complicated relationship between colorectal epithelium and surrounding environment. C4 cells were featured with high invasive potential and related with TAMs and CAFs, and further validated in vitro using IHC and mIHC.

Additional file 2 of Decoding the colorectal cancer ecosystem emphasizes the cooperative role of cancer cells, TAMs and CAFsin tumor progression

Rongfang Shen, Ping Li, Botao Zhang, Lin Feng & Shujun Cheng
Additional file 2: Table S2. Cellular annotation and clinical characteristic of SMC and KUL3 cohort. Relate to Figure 1 and Figure S1.

Additional file 3 of Decoding the colorectal cancer ecosystem emphasizes the cooperative role of cancer cells, TAMs and CAFsin tumor progression

Rongfang Shen, Ping Li, Botao Zhang, Lin Feng & Shujun Cheng
Additional file 3: Table S3. Representative marker genes used for cell type annotation.

Additional file 13 of Decoding the colorectal cancer ecosystem emphasizes the cooperative role of cancer cells, TAMs and CAFsin tumor progression

Rongfang Shen, Ping Li, Botao Zhang, Lin Feng & Shujun Cheng
Additional file 13: Figure S6. Characterization of stromal cells in the SMC cohort. A. UMAP plot of stromal cells colored by cell cluster and sample origin. B. Heat map of marker genes identified through Seurat. For each cell cluster, cells were down-sampled to 100. C. Differentiation trajectories inferred by Monocle2. Dots represent stromal cells and are colored by identified cell cluster. D. Heat map of the top 5 ranked regulons in S5 and S6. E....

Additional file 6 of Decoding the colorectal cancer ecosystem emphasizes the cooperative role of cancer cells, TAMs and CAFsin tumor progression

Rongfang Shen, Ping Li, Botao Zhang, Lin Feng & Shujun Cheng
Additional file 6: Table S6. Identified meta-programs and its biological process annotation. Related to Figure 3F, Figure S2B.

Additional file 6 of Decoding the colorectal cancer ecosystem emphasizes the cooperative role of cancer cells, TAMs and CAFsin tumor progression

Rongfang Shen, Ping Li, Botao Zhang, Lin Feng & Shujun Cheng
Additional file 6: Table S6. Identified meta-programs and its biological process annotation. Related to Figure 3F, Figure S2B.

Additional file 7 of Decoding the colorectal cancer ecosystem emphasizes the cooperative role of cancer cells, TAMs and CAFsin tumor progression

Rongfang Shen, Ping Li, Botao Zhang, Lin Feng & Shujun Cheng
Additional file 7: Table S7. Key resource table.

Additional file 8 of Decoding the colorectal cancer ecosystem emphasizes the cooperative role of cancer cells, TAMs and CAFsin tumor progression

Rongfang Shen, Ping Li, Botao Zhang, Lin Feng & Shujun Cheng
Additional file 8: Figure S1. Cellular landscape of CRC in the KUL3 cohort. A. UMAP plot of 26,268 cells colored by cell cluster, CMS and sample origin. Each dot represents a cell and cellular cluster is annotated with text. B. Proportions of the identified cell clusters distributed across tumor, border and adjacent normal tissues with the relative cell type proportions and total cell numbers. Upper: all cell clusters; lower: immune and stromal cell clusters. C....

Additional file 9 of Decoding the colorectal cancer ecosystem emphasizes the cooperative role of cancer cells, TAMs and CAFsin tumor progression

Rongfang Shen, Ping Li, Botao Zhang, Lin Feng & Shujun Cheng
Additional file 9: Figure S2. Functional heterogeneity of CRC epithelial cells in the SMC cohort. A. UMAP feature plot of the top 10 upregulated genes in the SMC cohort. B. Correlation heat map of 123 programs identified by cNMF. The Pearson correlation coefficient is indicated by the color. C. Heatmap of the relative mean signature score of cancer cell functional signatures across C1-C7. The signature score was calculated using the “AUCell” package. D. Heatmap of...

Daidzein stimulates fatty acid-induced fat deposition in C2C12 myoblast cells via the G protein-coupled receptor 30 pathway

Chengjian Zhou, Ping Li, Meihong Han & Xuejun Gao
Fat deposition in skeletal muscle is an important aspect of improving meat quality. Isoflavones can promote animal anabolism, but whether and how they regulate muscle fat deposition remain largely unclear. In this study, we explored the role and corresponding molecular mechanism of one of the major isoflavones, daidzein, in fat deposition in C2C12 myoblast cells. In the absence of fatty acids (FAs), daidzein did not promote triglyceride synthesis and lipid droplet formation in cells but...

The lipoprotein NlpD in Cronobacter sakazakii responds to acid stress and regulates macrophage resistance and virulence by maintaining membrane integrity

Xuemeng Ji, Ping Lu, Juan Xue, Ning Zhao, Yan Zhang, Lu Dong, Xuejiao Zhang, Ping Li, Yaozhong Hu, Jin Wang, Bowei Zhang, Jingmin Liu, Huan lv & Shuo Wang
Cronobacter sakazakii, an emerging opportunistic pathogen, is implicated in severe foodborne outbreak infections in premature and full-term infants. Generally, acid tolerance is vital for the pathogenesis of foodborne pathogens; however, its role in C. sakazakii virulence remains largely unknown. To screen out acid-tolerance determinants from transposon mutants, anovel counterselection method using gentamicin and acid was developed. Using the counterselection method and growth assay, we screened several acid-sensitive mutants and found that nlpD encodes an acid-resistance...

Convergence of carbapenem resistance and hypervirulence in a highly-transmissible ST11 clone of K. pneumoniae: An epidemiological, genomic and functional study

Ping Li, Qiqiang Liang, Wugao Liu, Beiwen Zheng, Lizhang Liu, Wei Wang, Zhijiang Xu, Man Huang & Youjun Feng
Co-occurrence of hypervirulence and KPC-2 carbapenem resistant phenotypes in a highly-transmissible ST11 clone ofKlebsiella pneumoniae has elicited deep concerns from public health stand point. To address this puzzle, we conducted a large-scale epidemiological, clinical and genomic study of K. pneumonia ST11 clones with both hypervirulence and carbapenem resistance in two tertiary hospitals in Zhejiang province. Most of the patients (15/23) were diagnosed with exclusively carbapenem-resistant K. pneumoniae (CRKP) infections. Ten death cases were reported, some...

Fostering Marine Biodiversity Data Sharing for Decision-Making in the Western Indian Ocean Region

Désirée Schwindenhammer, Hauke Kegler, Hauke Reuter, Christopher Muhando, Daudi Msagameno, George Rushingisha, Arthur Tuda, Theuri Mwangi & David Obura
This policy brief informs decision-makers about the benefits of effective marine biodiversity data sharing and proposes measures to encourage and improve sharing among stakeholders. The oceans and coastal areas in Eastern African countries are home to an abundance of marine biodiversity, with immense ecological and socioeconomic value. Stakeholders have varying interests concerning shared ecosystems. Transboundary conservation goals and harmonised coastal management strategies are of great value to sustain ecological services for future generations and to...

Short- and long-term follow-up outcomes of patients with Brucella endocarditis: a systematic review of 207 Brucella endocarditis Cases

Xiufeng Li, Tan Wang, Yuanzhi Wang, Songsong Xie, Wenbo Tan & Ping Li
Brucella endocarditis is a fatal complication and the most frequent cause of death for human brucellosis. This study aimed to systematically review the literature on the follow-up outcomes of Brucella endocarditis and analyze the determinants affecting the follow-up outcomes. The databases PubMed, Web of Science, Embase, and Cochrane were searched using keywords and suitable combinations. All studies reporting the follow-up outcomes of Brucella endocarditis were included. Finally, a total of 76 studies (207 patients), including...

Additional file 6 of Copy number variant analysis for syndromic congenital heart disease in the Chinese population

Ping Li, Weicheng Chen, Mengru Li, Zhengshan Zhao, Zhiyu Feng, Han Gao, Meijiao Suo, Ziqing Xu, Guixiang Tian, Feizhen Wu, Sheng Wei & Guoying Huang
Additional file 6. Table S4. CNVs in studies of syndromic CHD from different countries or ethnicities.

Copy number variant analysis for syndromic congenital heart disease in the Chinese population

Ping Li, Weicheng Chen, Mengru Li, Zhengshan Zhao, Zhiyu Feng, Han Gao, Meijiao Suo, Ziqing Xu, Guixiang Tian, Feizhen Wu, Sheng Wei & Guoying Huang
Abstract Background Syndromic congenital heart disease (CHD) is among the most severe conditions in the pediatric population. Copy number variant (CNV) is an important cause of syndromic CHD, but few studies focused on CNVs related to these patients in China. The present study aimed to identify pathogenic CNVs associated with syndromic CHD in the Chinese population. Methods A total of 109 sporadic patients with syndromic CHD were applied chromosomal microarray analysis (CMA). Phenotype spectrum of...

Additional file 1 of Chemometrics integrated with in silico pharmacology to reveal antioxidative and anti-inflammatory markers of dandelion for its quality control

Feng-Jie Liu, Jiao Yang, Xu-Yan Chen, Ting Yu, Hui Ni, Liang Feng, Ping Li & Hui-Jun Li
Additional file 1: Table S1. The identification of phenolic components in TH.Table S2. Antioxidant capacity of candidate markers. Table S3. The in silico pharmacokinetic parametersof candidate markers. Table S4. Methodology investigation for thequantitation of four markers. Figure S1. Representative UV absorbanceprofile (a), and base peak chromatogram (b). Figure S2. PLSRmodels. The summary of fit (a-c) and permutation tests (d-f) forantioxidative activity by DPPH and FRAP, and anti-inflammatory activity,respectively. Figure S3. The toxicity of luteolin (a),...

Editing of the rice importin gene IMPα1b results in sequestration of TAL effectors from plant cell nuclei

Jinfeng Peng, Jingyuan Nie, Xiaochen Chen, Liyuan Zhang, Xiaohui Yao, Ping Li, Huicong Shi, Congfeng Song & Hansong Dong
Abstract Transcription activator-like effectors (TALEs) produced by plant pathogenic bacteria mainly belonging to the genus Xanthomonas cause plant diseases through activation of host susceptibility genes in plant cell nuclei. How TALEs enter plant cell nuclei was not clear until recent studies about PthXo1 and TALI, two TALEs produced by Xanthomonas oryzae pv. oryzae (Xoo) and X. oryzae pv. oryzicola (Xoc), the rice (Oryza sativa) pathogens that cause bacterial blight and bacterial leaf streak, respectively. Here,...

Additional file 10 of Copy number variant analysis for syndromic congenital heart disease in the Chinese population

Ping Li, Weicheng Chen, Mengru Li, Zhengshan Zhao, Zhiyu Feng, Han Gao, Meijiao Suo, Ziqing Xu, Guixiang Tian, Feizhen Wu, Sheng Wei & Guoying Huang
Additional file 10. Table S7. Recurrent CNVs in previously published syndromic CHD cohorts and our study.

Additional file 1 of Copy number variant analysis for syndromic congenital heart disease in the Chinese population

Ping Li, Weicheng Chen, Mengru Li, Zhengshan Zhao, Zhiyu Feng, Han Gao, Meijiao Suo, Ziqing Xu, Guixiang Tian, Feizhen Wu, Sheng Wei & Guoying Huang
Additional file 1. Table S1. Summary of tools for candidate gene prioritization, including VarElect, OVA, AMELIE, and ToppGene.

Early-life antibiotic exposure increases the risk of childhood overweight and obesity in relation to dysbiosis of gut microbiota: a birth cohort study

Ping Li, Xuelian Chang, Xiaoyu Chen, Chuan Wang, Yu Shang, Dongyi Zheng & Kemin Qi
Abstract Background Early-life antibiotic exposure is associated with the development of later obesity through the disruption of gut microbiota in the animal models. However, the related epidemiological evidence is still conflicting. Methods A birth cohort was consisted of 2140 mother-infant pairs in Chaoyang District Maternal and Child Health Care Hospital in this study. Here, their available antibiotic exposure during the first one year of life was ascertained using a open-ended questionnaire and related anthropometric parameters...

Predictive Value of Adenoid-Nasopharyngeal Ratio in the Diagnosis of Secretory Otitis Media

Ping Li, Tao Li, Liang Yu, Aiping Chen, Yisha Wu, Yuzhu Wan & Li Shi
ObjectivesTo explore the associated factors of otitis media with effusion (OME) and analyze the diagnostic value of the adenoid-nasopharyngeal (A/N) ratio to OME.MethodsPatients with adenoid hypertrophy (AH) recently in 2 years were collected, including sex, age, duration, with/without rhinosinusitis, and examination results, including Cone Beam Computerized Tomography (CBCT) sinus imaging, tympanometry, pure tone audiometry (PTA), blood test, and allergen detection. According to Liden/Jerger’s classification, the patients were divided into two groups: Type B and type...

Additional file 2 of Editing of the rice importin gene IMPα1b results in sequestration of TAL effectors from plant cell nuclei

Jinfeng Peng, Jingyuan Nie, Xiaochen Chen, Liyuan Zhang, Xiaohui Yao, Ping Li, Huicong Shi, Congfeng Song & Hansong Dong
Additional file 2. Figure S1. Split-ubiquitin-based yeast two-hybrid (SUB-Y2H) and luciferin (Luc) living fluorescence imaging (LLFI) assays of protein combinations between PthXo1 and different variants of OsIMPα1b and OsIMPα1a (shown as IMPα1b and IMPα1a in this figure). Figure S2. CRISPR/Cas9-based OsIMPα1a gene editing and viability of OsIMPα1a-edited (OsIMPα1a-ED) and OsIMPα1b-edited (OsIMPα1b-ED) rice lines. Figure S3. Plants growing in the specific rice-growing pond and representing plant populations of the wild type (Nipponbare) and OsIMPα1b-edited lines (OsIMPα1b-ED#6...

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  • University of Dar es Salaam
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