501 Works

Additional file 29 of Proteogenomic insights into the biology and treatment of pancreatic ductal adenocarcinoma

Yexin Tong, Mingjun Sun, Lingli Chen, Yunzhi Wang, Yan Li, Lingling Li, Xuan Zhang, Yumeng Cai, Jingbo Qie, Yanrui Pang, Ziyan Xu, Jiangyan Zhao, Xiaolei Zhang, Yang Liu, Sha Tian, Zhaoyu Qin, Jinwen Feng, Fan Zhang, Jiajun Zhu, Yifan Xu, Wenhui Lou, Yuan Ji, Jianyuan Zhao, Fuchu He, Yingyong Hou … & Chen Ding
Additional file 29: Table S7. Characterization of Immune Infiltration in PDAC. Table S7A Matrix of xCell signatures significantly altered in 5 immune subgroups. Table S7B Matrix describing the expression of proteins in 5 immune subgroups. Table S7C Matrix of GSVA scores of pathways significantly altered in 5 immune subgroups, transcriptome level. Table S7D Matrix of amplification/deletion events of genes in 5 immune subgroups. Table S7E Matrix describing the expression of proteins involved in TCA cycle.

Additional file 30 of Proteogenomic insights into the biology and treatment of pancreatic ductal adenocarcinoma

Yexin Tong, Mingjun Sun, Lingli Chen, Yunzhi Wang, Yan Li, Lingling Li, Xuan Zhang, Yumeng Cai, Jingbo Qie, Yanrui Pang, Ziyan Xu, Jiangyan Zhao, Xiaolei Zhang, Yang Liu, Sha Tian, Zhaoyu Qin, Jinwen Feng, Fan Zhang, Jiajun Zhu, Yifan Xu, Wenhui Lou, Yuan Ji, Jianyuan Zhao, Fuchu He, Yingyong Hou … & Chen Ding
Additional file 30: Table S8. HOGA1 inactivation promotes pancreatic cancer growth through activating LARP7-CDK1 pathway. Table S8A Quantified western blot results of 12 pairs of samples. Table S8B Proliferation of PANC-1 and BxPC-3 cells associated with HOGA1 knocked down. Table S8C Proliferation of PANC-1 and BxPC-3 cells associated with HOGA1 overexpressed. Table S8D Proliferation of PANC-1 and BxPC-3 cells associated with metabolic enzyme treatment. Table S8E A list of 773 different proteins detected in PANC-1...

Additional file 30 of Proteogenomic insights into the biology and treatment of pancreatic ductal adenocarcinoma

Yexin Tong, Mingjun Sun, Lingli Chen, Yunzhi Wang, Yan Li, Lingling Li, Xuan Zhang, Yumeng Cai, Jingbo Qie, Yanrui Pang, Ziyan Xu, Jiangyan Zhao, Xiaolei Zhang, Yang Liu, Sha Tian, Zhaoyu Qin, Jinwen Feng, Fan Zhang, Jiajun Zhu, Yifan Xu, Wenhui Lou, Yuan Ji, Jianyuan Zhao, Fuchu He, Yingyong Hou … & Chen Ding
Additional file 30: Table S8. HOGA1 inactivation promotes pancreatic cancer growth through activating LARP7-CDK1 pathway. Table S8A Quantified western blot results of 12 pairs of samples. Table S8B Proliferation of PANC-1 and BxPC-3 cells associated with HOGA1 knocked down. Table S8C Proliferation of PANC-1 and BxPC-3 cells associated with HOGA1 overexpressed. Table S8D Proliferation of PANC-1 and BxPC-3 cells associated with metabolic enzyme treatment. Table S8E A list of 773 different proteins detected in PANC-1...

Additional file 13 of Proteogenomic insights into the biology and treatment of pancreatic ductal adenocarcinoma

Yexin Tong, Mingjun Sun, Lingli Chen, Yunzhi Wang, Yan Li, Lingling Li, Xuan Zhang, Yumeng Cai, Jingbo Qie, Yanrui Pang, Ziyan Xu, Jiangyan Zhao, Xiaolei Zhang, Yang Liu, Sha Tian, Zhaoyu Qin, Jinwen Feng, Fan Zhang, Jiajun Zhu, Yifan Xu, Wenhui Lou, Yuan Ji, Jianyuan Zhao, Fuchu He, Yingyong Hou … & Chen Ding
Additional file 13: Fig. S13. Proteomic subtypes divided early-stage PDAC patients into subtypes with different prognosis, related to Fig. 6. A Summary of the relationship between proteomic subtypes and TNM stage subtypes. B Kaplan-Meier curves for overall survival of early-stage (IA and IB) PDAC patients based on 3 proteomic subtypes (log-rank test). C Bar plot indicating the enriched pathways in early-stage patients who were divided into three proteomic subtypes. D Heatmap of differentially expressed kinase...

Additional file 15 of Proteogenomic insights into the biology and treatment of pancreatic ductal adenocarcinoma

Yexin Tong, Mingjun Sun, Lingli Chen, Yunzhi Wang, Yan Li, Lingling Li, Xuan Zhang, Yumeng Cai, Jingbo Qie, Yanrui Pang, Ziyan Xu, Jiangyan Zhao, Xiaolei Zhang, Yang Liu, Sha Tian, Zhaoyu Qin, Jinwen Feng, Fan Zhang, Jiajun Zhu, Yifan Xu, Wenhui Lou, Yuan Ji, Jianyuan Zhao, Fuchu He, Yingyong Hou … & Chen Ding
Additional file 15: Fig. S15. Protein markers for three PDAC proteomic subtypes, related to Fig. 6. A The boxplot indicating the comparison of tumor purity across the proteomic subtypes. B Heatmap indicating the expression of protein biomarkers in the three proteomic subtypes. C Kaplan-Meier curves for overall survival based on proteomic abundance of ACOX1, S100A4 and MCM6 (log-rank test). D IHC profiling of proteomic subtype markers in PDAC. FFPE sections were stained for ACOX1, S100A4...

Additional file 16 of Proteogenomic insights into the biology and treatment of pancreatic ductal adenocarcinoma

Yexin Tong, Mingjun Sun, Lingli Chen, Yunzhi Wang, Yan Li, Lingling Li, Xuan Zhang, Yumeng Cai, Jingbo Qie, Yanrui Pang, Ziyan Xu, Jiangyan Zhao, Xiaolei Zhang, Yang Liu, Sha Tian, Zhaoyu Qin, Jinwen Feng, Fan Zhang, Jiajun Zhu, Yifan Xu, Wenhui Lou, Yuan Ji, Jianyuan Zhao, Fuchu He, Yingyong Hou … & Chen Ding
Additional file 16: Fig. S16. Characterization of immune infiltration in PDAC, related to Fig. 7. A Boxplot showing the age among five immune clusters. B Heatmap of xCell score between samples in old/young group of TCGA cohort. C Distribution of the percentage of proteomics subtypes across different immune subtypes (Fisher’s exact test). D The Sankey plot revealing the association between proteomics subtypes and immune subtypes. E Kaplan-Meier curves for overall survival based on immune subtypes...

Additional file 17 of Proteogenomic insights into the biology and treatment of pancreatic ductal adenocarcinoma

Yexin Tong, Mingjun Sun, Lingli Chen, Yunzhi Wang, Yan Li, Lingling Li, Xuan Zhang, Yumeng Cai, Jingbo Qie, Yanrui Pang, Ziyan Xu, Jiangyan Zhao, Xiaolei Zhang, Yang Liu, Sha Tian, Zhaoyu Qin, Jinwen Feng, Fan Zhang, Jiajun Zhu, Yifan Xu, Wenhui Lou, Yuan Ji, Jianyuan Zhao, Fuchu He, Yingyong Hou … & Chen Ding
Additional file 17: Fig. S17. The impact of FH amplification in PDAC, related to Fig. 7. A Scatter plot on the left presents the correlation between FH copy number and FH expression in TCGA cohort (left) or in WSU cohort (right). B, C The bar plot shows the distribution of patients with FH amplification between diabetes and non-diabetes in our cohort (B), in TCGA cohort (C, left) and in WSU cohort (C, right). D The...

Additional file 4 of Expanding known viral diversity in plants: virome of 161 species alongside an ancient canal

Shixing Yang, Qingqing Mao, Yan Wang, Jingxian He, Jie Yang, Xu Chen, Yuqing Xiao, Yumin He, Min Zhao, Juan Lu, Zijun Yang, Ziyuan Dai, Qi Liu, Yuxin Yao, Xiang Lu, Hong Li, Rui Zhou, Jian Zeng, Wang Li, Chenglin Zhou, Xiaochun Wang, Quan Shen, Hui Xu, Xutao Deng, Eric Delwart … & Wen Zhang
Additional file 4. Table S2: Information of viruses with complete genomes determined in the present study.

Additional file 4 of Expanding known viral diversity in plants: virome of 161 species alongside an ancient canal

Shixing Yang, Qingqing Mao, Yan Wang, Jingxian He, Jie Yang, Xu Chen, Yuqing Xiao, Yumin He, Min Zhao, Juan Lu, Zijun Yang, Ziyuan Dai, Qi Liu, Yuxin Yao, Xiang Lu, Hong Li, Rui Zhou, Jian Zeng, Wang Li, Chenglin Zhou, Xiaochun Wang, Quan Shen, Hui Xu, Xutao Deng, Eric Delwart … & Wen Zhang
Additional file 4. Table S2: Information of viruses with complete genomes determined in the present study.

supplementary Information version 15 from Investigation of the photoluminescent properties, scintillation behaviour and toxicological profile of various magnesium tungstate nanoscale motifs

Nathaniel Hurley, Sailesh Srinivas, Justin Fang, Manli Sun, Simon Hong, Chia Te Chien, Alan Guo, Tamor A. Khan, Mingxing Li, Mircea Cotlet, Federico Moretti, Edith Bourret-Courchesne, Daniel Radin, Stella E. Tsirka, Maya Shelly & Stanislaus S. Wong
We have synthesized several morphologies and crystal structures of MgWO4 using a one-pot hydrothermal method, producing not only monoclinic stars and large nanoparticles but also triclinic wool balls and sub-10 nm nanoparticles. Herein we describe the importance of reaction parameters in demonstrating morphology control of as-prepared MgWO4. Moreover, we correlate structure and composition with the resulting photoluminescence and radioluminescence properties. Specifically, triclinic-phase samples yielded a photoluminescence emission of 421 nm, whereas monoclinic-phase materials gave rise...

Supplementary document for Unambiguous spectral characterization on triplet energy transfer from quantum dots mediated by hole transfer competing with other carrier dynamics - 6173732.pdf

Lei Wang, Gaoyuan Yang, Boyu Zhang, Xin Zhang, Dezheng Liu, Ying Liang & Guijie Liang
Supplement 1

sj-docx-1-pac-10.1177_18344909221142368 - Supplemental material for The beneficial effect of growth mindset intervention for adolescents in economically disadvantaged areas of China

Ruixue Xia, Peiying Zhang, Ruiyang Liu, Junwei Xue, Huijing Zhu, Guaiguai Guo, Min Zhang & Yang Liu
Supplemental material, sj-docx-1-pac-10.1177_18344909221142368 for The beneficial effect of growth mindset intervention for adolescents in economically disadvantaged areas of China by Ruixue Xia, Peiying Zhang, Ruiyang Liu, Junwei Xue, Huijing Zhu, Guaiguai Guo, Min Zhang and Yang Liu in Journal of Pacific Rim Psychology

Unambiguous spectral characterization on triplet energy transfer from quantum dots mediated by hole transfer competing with other carrier dynamics

Lei Wang, Gaoyuan Yang, Boyu Zhang, Xin Zhang, Dezheng Liu, Ying Liang & Guijie Liang
Triplet generation by QDs-sensitized molecules emerges great potential in many applications. However, the mechanism of triplet energy transfer (TET) is still fuzzy especially due to complicated energy level alignment of QDs and molecules or trap states in QDs. Here, CdSe QDs and 5-tetracene carboxylic acid (TCA) molecules are selected as the triplet donor and acceptor, respectively, to form a TET system. By tuning the band gap of CdSe, the CdSe-TCA complex is exactly designed to...

sj-docx-1-jiv-10.1177_08862605221138655 – Supplemental material for Exploring Collaborative Care Effects on the Mental and Physical Health of Patients With and Without Violent Victimization Histories

Keith L. Hullenaar, Frederick P. Rivara, Jin Wang & Douglas F. Zatzick
Supplemental material, sj-docx-1-jiv-10.1177_08862605221138655 for Exploring Collaborative Care Effects on the Mental and Physical Health of Patients With and Without Violent Victimization Histories by Keith L. Hullenaar, Frederick P. Rivara, Jin Wang and Douglas F. Zatzick in Journal of Interpersonal Violence

sj-docx-2-jiv-10.1177_08862605221138655 – Supplemental material for Exploring Collaborative Care Effects on the Mental and Physical Health of Patients With and Without Violent Victimization Histories

Keith L. Hullenaar, Frederick P. Rivara, Jin Wang & Douglas F. Zatzick
Supplemental material, sj-docx-2-jiv-10.1177_08862605221138655 for Exploring Collaborative Care Effects on the Mental and Physical Health of Patients With and Without Violent Victimization Histories by Keith L. Hullenaar, Frederick P. Rivara, Jin Wang and Douglas F. Zatzick in Journal of Interpersonal Violence

Additional file 1 of Nitidine chloride induces caspase 3/GSDME-dependent pyroptosis by inhibting PI3K/Akt pathway in lung cancer

Fei Yu, Weidan Tan, Zhiquan Chen, Xiaoju Shen, Xiaoxiang Mo, Xiaocheng Mo, Jingchuan He, Zhihua Deng, Jie Wang, Zhuo Luo & Jie Yang
Additional file 1: Table S1 The overlapped targets between NC and lung cancer. Fig. S1 A–C GSDMC, GSDMD and GSDME protein expression were analyzed by Western blotting. D WB analyses of GSDMC, GSDMD and GSDME in lung cancer cell lines and BEAS-2B cell line. Protein levels are expressed as mean ± SD (n=3). Fig. S2 H1688 or A549 cells were transfected with siRNA targeting caspase 3 (siRNA-cas3-1/2/3) or control siRNA for 24 h. Fig. S3...

RETRACTED ARTICLE: KIAA1429 promotes osteosarcoma progression by promoting stem cell properties and is regulated by miR-143-3p

Qicai Han, Jie Yang, Hao Yang, Chao Li, Juan Li & Yuan Cao
We, the Editors and Publisher of the journal Cell Cycle, have retracted the following article: Qicai Han, Jie Yang, Hao Yang, Chao Li, Juan Li & Yuan Cao (2020) KIAA1429 promotes osteosarcoma progression by promoting stem cell properties and is regulated by miR-143-3p, Cell Cycle, 19:10, 1172-1185, DOI: 10.1080/15384101.2020.1749465 Since publication, concerns have been raised about similarity of the data in another published article: Yang J, Han Q, Li C, Yang H, Chen X, Wang...

Using GBIF to Demonstrate Colonial Legacies on Biodiversity Data

Ryan S. Mohammed, Melissa Kemp, Michelle J. LeFebvre, Alexis M. Mychajliw, Grace Turner, Kelly Fowler, Michael Pateman, Maria A. Nieves-Colón, Lanya Fanovich, Siobhan B. Cooke, Liliana M. Dávalos, Scott M. Fitzpatrick, Christina M. Giovas, Myles Stokowski & Ashley A. Wrean
Biologists recognize the Caribbean archipelago as a biodiversity hotspot and employ it for their research as a “natural laboratory”, but do not always appreciate that these ecosystems are in fact palimpsests shaped by multiple human cultures over millennia. We discuss two case studies of the Caribbean’s fragmented natural history collections, the effects of differing legislation and governance by the region’s multiple nation states. We use digital natural history specimen data from GBIF to demonstrate how...

Bidirectional regulation of structural damage on autophagy in the C. elegans epidermis

Rong Fu, Xiaowan Jiang, Yuyan Yang, Chunxia Wang, Yun Zhang, Yi Zhu & Huimin Zhang
A variety of disturbances such as starvation, organelle damage, heat stress, hypoxia and pathogen infection can influence the autophagic process. However, how the macroautophagy/autophagy machinery is regulated intrinsically by structural damage of the cell remains largely unknown. In this work, we utilized the C. elegans epidermis as the model to address this question. Our results showed that structural damage by mechanical wounding exerted proximal inhibitory effect and distant promotional effect on autophagy within the same...

Robust statistical inference for longitudinal data with nonignorable dropouts

Yujing Shao, Wei Ma & Lei Wang
In this paper, we propose robust statistical inference and variable selection method for generalized linear models that accommodate the outliers, nonignorable dropouts and within-subject correlations. The purpose of our study is threefold. First, we construct the robust and bias-corrected generalized estimating equations (GEEs) by combining the Mallows-type weights, Huber's score function and inverse probability weighting approaches to against the influence of outliers and account for nonignorable dropouts. Subsequently, the generalized method of moments is utilized...

Damage of brown planthopper (BPH) Nilaparvata lugens and rice leaf folder (LF) Cnaphalocrocis medinalis in parent plants lead to distinct resistance in ratoon rice

Qian-Qian Deng, Mao Ye, Xiao-Bao Wu, Jia Song, Jun Wang, Li-Na Chen, Zhong-Yan Zhu & Jing Xie
Herbivore-induced defense responses are often specific, whereas plants could induce distinct defense responses corresponding to infestation by different herbivorous insects. Brown plant hopper (BPH) Nilaparvata lugens, a phloem-feeding insect, and rice leaf folder (LF) Cnaphalocrocis medinalis, a chewing insect, are both specialist herbivores on rice. To characterize the distinct resistance primed by prior damage to these two specialist herbivores, we challenged rice plants with two herbivores during vegetative growth of parent plants and assessed plant...

Damage of brown planthopper (BPH) Nilaparvata lugens and rice leaf folder (LF) Cnaphalocrocis medinalis in parent plants lead to distinct resistance in ratoon rice

Qian-Qian Deng, Mao Ye, Xiao-Bao Wu, Jia Song, Jun Wang, Li-Na Chen, Zhong-Yan Zhu & Jing Xie
Herbivore-induced defense responses are often specific, whereas plants could induce distinct defense responses corresponding to infestation by different herbivorous insects. Brown plant hopper (BPH) Nilaparvata lugens, a phloem-feeding insect, and rice leaf folder (LF) Cnaphalocrocis medinalis, a chewing insect, are both specialist herbivores on rice. To characterize the distinct resistance primed by prior damage to these two specialist herbivores, we challenged rice plants with two herbivores during vegetative growth of parent plants and assessed plant...

A role for myosin II cluster and membrane energy in cortex rupture for Dictyostelium discoideum cells

Emmanuel Asante-Asamani, Daniel Grange, Devarshi Rawal, Zully Santiago, John Loustau & Derrick Brazill
Blebs, pressure driven protrusions of the cell membrane, facilitate the movement of eukaryotic cells such as the soil amoeba Dictyostelium discoideum, white blood cells and cancer cells. Blebs initiate when the cell membrane separates from the underlying cortex. A local rupture of the cortex, has been suggested as a mechanism by which blebs are initiated. However, much clarity is still needed about how cells inherently regulate rupture of the cortex in locations where blebs are...

Untargeted metabolomics profiling in a mouse model of lung cancer treated with thermal ablation

Haoyue Pang, Kaiwen Hu, Fuyao Li, Hua Duan, Yu Chen, Yaqi Hu, Dan Wang & Min Jiang
Thermal ablation is widely used in the treatment of lung cancer and is beneficial for the overall survival of patients in clinic. However, there is barely a priority in which ablation system should be chosen under different periods of tumor progression in lung cancer. The present study investigated different modes of thermal ablation systems in mice with transplanted Lewis lung carcinoma tumors and their various biological effects in local regions using untargeted metabolomics. The results...

Untargeted metabolomics profiling in a mouse model of lung cancer treated with thermal ablation

Haoyue Pang, Kaiwen Hu, Fuyao Li, Hua Duan, Yu Chen, Yaqi Hu, Dan Wang & Min Jiang
Thermal ablation is widely used in the treatment of lung cancer and is beneficial for the overall survival of patients in clinic. However, there is barely a priority in which ablation system should be chosen under different periods of tumor progression in lung cancer. The present study investigated different modes of thermal ablation systems in mice with transplanted Lewis lung carcinoma tumors and their various biological effects in local regions using untargeted metabolomics. The results...

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