232 Works

Blood DNA methylation signatures are associated with social determinants of health among survivors of childhood cancer

Nan Song, Jin-Ah Sim, Qian Dong, Yinan Zheng, Lifang Hou, Zhenghong Li, Chia-Wei Hsu, Haitao Pan, Heather Mulder, John Easton, Emily Walker, Geoffrey Neale, Carmen L. Wilson, Kirsten K. Ness, Kevin R. Krull, Deo Kumar Srivastava, Yutaka Yasui, Jinghui Zhang, Melissa M. Hudson, Leslie L. Robison, I-Chan Huang & Zhaoming Wang
Social epigenomics is an emerging field in which social scientist collaborate with computational biologists, especially epigeneticists, to address the underlying pathway for biological embedding of life experiences. This social epigenomics study included long-term childhood cancer survivors enrolled in the St. Jude Lifetime Cohort. DNA methylation (DNAm) data were generated using the Illumina EPIC BeadChip, and three social determinants of health (SDOH) factors were assessed: self-reported educational attainment, personal income, and an area deprivation index based...

Estimating disability-adjusted life years for breast cancer and the impact of screening in female populations in China, 2015–2030: an exploratory prevalence-based analysis applying local weights

Xin-Xin Yan, Juan Zhu, Yan-Jie Li, Meng-Di Cao, Xin Wang, Hong Wang, Cheng-Cheng Liu, Jing Wang, Yang Li & Ju-Fang Shi
Abstract Background Most cancer disability-adjusted life year (DALY) studies worldwide have used broad, generic disability weights (DWs); however, differences exist among populations and types of cancers. Using breast cancer as example, this study aimed to estimate the population-level DALYs in females in China and the impact of screening as well as applying local DWs. Methods Using multisource data, a prevalence-based model was constructed. (1) Overall years lived with disability (YLDs) were estimated by using numbers...

Additional file 2 of Estimating disability-adjusted life years for breast cancer and the impact of screening in female populations in China, 2015–2030: an exploratory prevalence-based analysis applying local weights

Xin-Xin Yan, Juan Zhu, Yan-Jie Li, Meng-Di Cao, Xin Wang, Hong Wang, Cheng-Cheng Liu, Jing Wang, Yang Li & Ju-Fang Shi
Additional file 2: Clinical stage-specific disability weights and distribution of breast cancer in females in China.

Additional file 1 of Pseudomonas aeruginosa biofilm dispersion by the mouse antimicrobial peptide CRAMP

Yang Zhang, Peng Cheng, Shiyuan Wang, Xiaofen Li, Lianci Peng, Rendong Fang, Jing Xiong, Hui Li, Cui Mei, Jiye Gao, Zhenhui Song, Dengfeng Xu, Lizhi Fu, Chenghong Li, Xueqing Wu, Yuzhang He & Hongwei Chen
Additional file 1. Detailed methods or results covered in this article.

Additional file 4 of Pseudomonas aeruginosa biofilm dispersion by the mouse antimicrobial peptide CRAMP

Yang Zhang, Peng Cheng, Shiyuan Wang, Xiaofen Li, Lianci Peng, Rendong Fang, Jing Xiong, Hui Li, Cui Mei, Jiye Gao, Zhenhui Song, Dengfeng Xu, Lizhi Fu, Chenghong Li, Xueqing Wu, Yuzhang He & Hongwei Chen
Additional file 4. Differentially metabolic substance data.

Additional file 4 of Pseudomonas aeruginosa biofilm dispersion by the mouse antimicrobial peptide CRAMP

Yang Zhang, Peng Cheng, Shiyuan Wang, Xiaofen Li, Lianci Peng, Rendong Fang, Jing Xiong, Hui Li, Cui Mei, Jiye Gao, Zhenhui Song, Dengfeng Xu, Lizhi Fu, Chenghong Li, Xueqing Wu, Yuzhang He & Hongwei Chen
Additional file 4. Differentially metabolic substance data.

Pseudomonas aeruginosa biofilm dispersion by the mouse antimicrobial peptide CRAMP

Yang Zhang, Peng Cheng, Shiyuan Wang, Xiaofen Li, Lianci Peng, Rendong Fang, Jing Xiong, Hui Li, Cui Mei, Jiye Gao, Zhenhui Song, Dengfeng Xu, Lizhi Fu, Chenghong Li, Xueqing Wu, Yuzhang He & Hongwei Chen
Abstract Pseudomonas aeruginosa (P. aeruginosa) is a known bacterium that produces biofilms and causes severe infection. Furthermore, P. aeruginosa biofilms are extremely difficult to eradicate, leading to the development of chronic and antibiotic-resistant infections. Our previous study showed that a cathelicidin-related antimicrobial peptide (CRAMP) inhibits the formation of P. aeruginosa biofilms and markedly reduces the biomass of preformed biofilms, while the mechanism of eradicating bacterial biofilms remains elusive. Therefore, in this study, the potential mechanism...

BMSC exosome-enriched acellular fish scale scaffolds promote bone regeneration

Yangyufan Wang, Bin Kong, Xiang Chen, Rui Liu, Yuanjin Zhao, Zhuxiao Gu & Qing Jiang
Abstract Tissue engineering scaffolds are essential for repairing bone defects. The use of biomimetic scaffolds for bone tissue engineering has been investigated for decades. To date, the trend in this area has been moved toward the construction of biomimetic acellular scaffolds with effective modification to enhance the osteogenic differentiation efficiency of bone marrow mesenchymal stem cells (BMSCs). The exosomes derived from BMSCs have been shown as a potential therapeutic tool for repairing bone defects. In...

Effects of 24-epibrassinolide on the postharvest quality and antioxidant activities of blueberry fruits

Zhuo Min, Lu Jiang, Yimei Zhao, Xinye Wang, Qing Liu & Yang Zhang
In this study, blueberry fruits (Vaccinium corymbosum cv. ‘Bluerain’) were sprayed with different concentrations (0.25, 0.5, 0.75, and 1 mg/L) of exogenous 24-epibrassionolide (EBR) after harvest and kept at 18°C and relative humidity of 90∼95% for 8 d. By observing the decay incidence and firmness changes, the optimal treatment concentration (0.75 mg/L) was screened, and then the effects of 0.75 mg/L EBR treatment on fruit quality and antioxidant activities were further explored. The results showed...

Dietary supplementation of Macleaya cordata extract and Bacillus in combination improve laying performance by regulating reproductive hormones, intestinal microbiota and barrier function of laying hens

Fei Wang, Peng Zou, Shujie Xu, Qi Wang, Yuanhao Zhou, Xiang Li, Li Tang, Baikui Wang, Qian Jin, Dongyou Yu & Weifen Li
Abstract Background This study aimed to investigate whether the combination of Macleaya cordata extract (MCE) and Bacillus could improve the laying performance and health of laying hens better. Methods A total of 360 29-week-old Jingbai laying hens were randomly divided into 4 treatments: control group (basal diet), MCE group (basal diet + MCE), Probiotics Bacillus Compound (PBC) group (basal diet + compound Bacillus), MCE + PBC group (basal diet + MCE + compound Bacillus). The...

Additional file 3 of Immune-related 3-lncRNA signature with prognostic connotation in a multi-cancer setting

Shimaa Sherif, Raghvendra Mall, Hossam Almeer, Adviti Naik, Abdulaziz Al Homaid, Remy Thomas, Jessica Roelands, Sathiya Narayanan, Mahmoud Gasim Mohamed, Shahinaz Bedri, Salha Bujassoum Al-Bader, Kulsoom Junejo, Davide Bedognetti, Wouter Hendrickx & Julie Decock
Additional file 3: Propagation walkscores of 127 proxy protein-coding genes in the TCGA-BRCA cohort.

Additional file 4 of Immune-related 3-lncRNA signature with prognostic connotation in a multi-cancer setting

Shimaa Sherif, Raghvendra Mall, Hossam Almeer, Adviti Naik, Abdulaziz Al Homaid, Remy Thomas, Jessica Roelands, Sathiya Narayanan, Mahmoud Gasim Mohamed, Shahinaz Bedri, Salha Bujassoum Al-Bader, Kulsoom Junejo, Davide Bedognetti, Wouter Hendrickx & Julie Decock
Additional file 4: Canonical pathways, diseases and functions associated with the 127 proxy protein-coding genes.

CTCF-AID2

Beisi Xu, Mohamed Nadhir Djekidel, Chunliang Li & Justin Williams
Hi-C and HiChIP analyssi https://doi.org/10.6084/m9.figshare.21002533 CHIPSEQ QC https://doi.org/10.6084/m9.figshare.7411835

Ischemic stroke and intracranial hemorrhage in extracorporeal membrane oxygenation for COVID-19: A systematic review and meta-analysis

Yu Jin, Yang Zhang & Jinping Liu
PurposeExtracorporeal membrane oxygenation (ECMO) is employed to support critically ill COVD-19 patients. The occurrence of ischemic stroke and intracranial hemorrhage (ICH), as well as the implementation of anticoagulation strategies under the dual influence of ECMO and COVID-19 remain unclear. We conducted a systematic review and meta-analysis to describe the ischemic stroke, ICH and overall in-hospital mortality in COVID-19 patients receiving ECMO and summarize the anticoagulation regimens.MethodsEMBASE, PubMed, Cochrane, and Scopus were searched for studies examining...

Additional file 1 of Estimating disability-adjusted life years for breast cancer and the impact of screening in female populations in China, 2015–2030: an exploratory prevalence-based analysis applying local weights

Xin-Xin Yan, Juan Zhu, Yan-Jie Li, Meng-Di Cao, Xin Wang, Hong Wang, Cheng-Cheng Liu, Jing Wang, Yang Li & Ju-Fang Shi
Additional file 1: Demographic, breast cancer epidemiological and screening factors of the female populations in China.

Additional file 6 of Immune-related 3-lncRNA signature with prognostic connotation in a multi-cancer setting

Shimaa Sherif, Raghvendra Mall, Hossam Almeer, Adviti Naik, Abdulaziz Al Homaid, Remy Thomas, Jessica Roelands, Sathiya Narayanan, Mahmoud Gasim Mohamed, Shahinaz Bedri, Salha Bujassoum Al-Bader, Kulsoom Junejo, Davide Bedognetti, Wouter Hendrickx & Julie Decock
Additional file 6: Prognostic value of ICR classifier across solid cancers. Forest plot showing HRs for death (overall survival) and corresponding 95%-confidence interval for the continuous ICR score and number of patients for each TCGA cancer cohort and RAQA breast cancer cohort. Significant positive HRs are visualized in blue and significant negative HRs are visualized in red. ICR enabled (HR < 1, p-value < 0.05) cancer types are indicated with orange asterisks and ICR disabled...

Immune-related 3-lncRNA signature with prognostic connotation in a multi-cancer setting

Shimaa Sherif, Raghvendra Mall, Hossam Almeer, Adviti Naik, Abdulaziz Al Homaid, Remy Thomas, Jessica Roelands, Sathiya Narayanan, Mahmoud Gasim Mohamed, Shahinaz Bedri, Salha Bujassoum Al-Bader, Kulsoom Junejo, Davide Bedognetti, Wouter Hendrickx & Julie Decock
Abstract Background Advances in our understanding of the tumor microenvironment have radically changed the cancer field, highlighting the emerging need for biomarkers of an active, favorable tumor immune phenotype to aid treatment stratification and clinical prognostication. Numerous immune-related gene signatures have been defined; however, their prognostic value is often limited to one or few cancer types. Moreover, the area of non-coding RNA as biomarkers remains largely unexplored although their number and biological roles are rapidly...

Additional file 7 of Immune-related 3-lncRNA signature with prognostic connotation in a multi-cancer setting

Shimaa Sherif, Raghvendra Mall, Hossam Almeer, Adviti Naik, Abdulaziz Al Homaid, Remy Thomas, Jessica Roelands, Sathiya Narayanan, Mahmoud Gasim Mohamed, Shahinaz Bedri, Salha Bujassoum Al-Bader, Kulsoom Junejo, Davide Bedognetti, Wouter Hendrickx & Julie Decock
Additional file 7: Akaike information criterion (AIC), delta AIC, and HRs for death (overall survival) and corresponding 95%-confidence interval for ICR and 3 ir-lncRNA signature in 18 solid cancer TCGA datasets and RAQA cohort.

Additional file 1 of DLC1 deficiency at diagnosis predicts poor prognosis in acute myeloid leukemia

Xueqian Li, Jiaqian Qi, Xiaofei Song, Xiaoyan Xu, Tingting Pan, Hong Wang, Jingyi Yang & Yue Han
Additional file 1: Figure S1. Correlation between gene significance and related module membership. A. The correlation between gene significance and module membership in the gray module. B. The correlation between gene significance and module membership in the blue module. *p < 0.05, **p < 0.01, ***p < 0.001.

Additional file 3 of DLC1 deficiency at diagnosis predicts poor prognosis in acute myeloid leukemia

Xueqian Li, Jiaqian Qi, Xiaofei Song, Xiaoyan Xu, Tingting Pan, Hong Wang, Jingyi Yang & Yue Han
Additional file 3: Figure S3. Identification of candidate hub genes to predict prognosis for AML patients. A. Partial likelihood deviance for different numbers of variables revealed by the LASSO regression model. Red dots represent the partial likelihood deviance values. Gray lines represent the partial likelihood deviance ± standard error. B. Fourteen candidate genes with minimum lambda values were obtained by LASSO regression with tenfold cross-validation. C. Candidate genes were filtrated from SVM-RFE algorithms. D. Five...

Additional file 4 of DLC1 deficiency at diagnosis predicts poor prognosis in acute myeloid leukemia

Xueqian Li, Jiaqian Qi, Xiaofei Song, Xiaoyan Xu, Tingting Pan, Hong Wang, Jingyi Yang & Yue Han
Additional file 4: Figure S4. The expression levels of DLC1, NFIB, DENND5B, TANC2, and ELAVL4 in AML patients with different survival status. Scatter plots of the five gene’s expression level in AML patients with different survival status based on GEO dataset. *p < 0.05, **p < 0.01, ***p < 0.001. Abbreviations: GEO, Gene Expression Omnibus.

Additional file 5 of DLC1 deficiency at diagnosis predicts poor prognosis in acute myeloid leukemia

Xueqian Li, Jiaqian Qi, Xiaofei Song, Xiaoyan Xu, Tingting Pan, Hong Wang, Jingyi Yang & Yue Han
Additional file 5: Figure S5. Kaplan-Meier survival curve according to the DLC1 expression level for 48 AML patients in our center. Kaplan-Meier plots was used to visualize the overall survival probability of 48 patients based on the expression of DLC1 at diagnosis in our center.

Additional file 6 of DLC1 deficiency at diagnosis predicts poor prognosis in acute myeloid leukemia

Xueqian Li, Jiaqian Qi, Xiaofei Song, Xiaoyan Xu, Tingting Pan, Hong Wang, Jingyi Yang & Yue Han
Additional file 6: Table S1. Clinical characteristics of 48 AML patients. Table S2. Basic information for the included GEO databases.

Additional file 13 of Exploration of the regulatory relationship between KRAB-Zfp clusters and their target transposable elements via a gene editing strategy at the cluster specific linker-associated sequences by CRISPR-Cas9

Yang Zhang, Fei He, Yanning Zhang, Qian Dai, Qintong Li, Jing Nan, Ruidong Miao & Bo Cheng
Additional file 13 Supplementary Table 5. sgRNA efficiency test in reporter system (raw data for Fig. 4B and D).

Additional file 3 of Exploration of the regulatory relationship between KRAB-Zfp clusters and their target transposable elements via a gene editing strategy at the cluster specific linker-associated sequences by CRISPR-Cas9

Yang Zhang, Fei He, Yanning Zhang, Qian Dai, Qintong Li, Jing Nan, Ruidong Miao & Bo Cheng
Additional file 3 Supplementary Fig. 3. The combined features about the zinc fingers (ZnFs) for all the mouse KRAB-ZFPs, including the composition specificity and frequency of occurrence. The detailed description is the same as that in Fig. 1C. Each row represents a single KRAB-ZFP.

Registration Year

  • 2022
    232

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Affiliations

  • St. Jude Children's Research Hospital
    232
  • Chinese Academy of Medical Sciences & Peking Union Medical College
    191
  • Fudan University
    170
  • Huazhong University of Science and Technology
    160
  • Soochow University
    148
  • Sun Yat-sen University
    136
  • Shanghai Jiao Tong University
    130
  • First Affiliated Hospital of Soochow University
    126
  • Tianjin Medical University
    106
  • Xinjiang Agricultural University
    106