| Publication |
Sentence |
Publish Date |
Extraction Date |
Species |
| Jiaxu Li, Yongjiao Han, Ning Zhao, Liping Lv, Ping Ma, Yangyang Zhang, Mingyuan Li, Hua Sun, Jiang Deng, Yanyu Zhan. Identification of immune- and oxidative stress-related signature genes as potential targets for mRNA vaccines for pancreatic cancer patients. Medicine. vol 103. issue 27. 2024-07-05. PMID:38968513. |
differentially expressed immune-related oxidative stress genes were screened via univariate cox regression analysis, and these genes were analyzed via nonnegative matrix factorization. |
2024-07-05 |
2024-07-08 |
Not clear |
| Yong Liu, Xiangwei Zhang, Zhaofei Pang, Yadong Wang, Haotian Zheng, Guanghui Wang, Kai Wang, Jiajun D. Prediction of prognosis and immunotherapy efficacy based on metabolic landscape in lung adenocarcinoma by bulk, single-cell RNA sequencing and Mendelian randomization analyses. Aging. vol 16. 2024-05-21. PMID:38771130. |
a matrix of metabolic pathway pairs was generated and a metabolic pathway-pair score (mpps) model was established by univariable, lasso, multivariable cox regression analyses. |
2024-05-21 |
2024-05-27 |
Not clear |
| Elvis Han Cui, Zizhao Zhang, Culsome Junwen Chen, Weng Kee Won. Applications of nature-inspired metaheuristic algorithms for tackling optimization problems across disciplines. Scientific reports. vol 14. issue 1. 2024-04-26. PMID:38658593. |
our applications are new and include finding maximum likelihood estimates of parameters in a single cell generalized trend model to study pseudotime in bioinformatics, estimating parameters in the commonly used rasch model in education research, finding m-estimates for a cox regression in a markov renewal model, performing matrix completion tasks to impute missing data for a two compartment model, and selecting variables optimally in an ecology problem in china. |
2024-04-26 |
2024-04-28 |
Not clear |
| Dan-Yang Chen, Yang-Yang Zhang, Hai-Hang Nie, Hai-Zhou Wang, Pei-Shan Qiu, Fan Wang, Ya-Nan Peng, Fei Xu, Qiu Zhao, Meng Zhan. Comprehensive analyses of solute carrier family members identify SLC12A2 as a novel therapy target for colorectal cancer. Scientific reports. vol 14. issue 1. 2024-02-23. PMID:38396064. |
we extracted the expression matrix of slc genes and established a prognostic model by univariate and multivariate cox regression. |
2024-02-23 |
2024-02-26 |
Not clear |
| Yijing Liu, Xiaodong He, Y I Yan. Tumor immune microenvironment-based clusters in predicting prognosis and guiding immunotherapy in breast cancer. Journal of biosciences. vol 49. 2024-01-30. PMID:38287674. |
after intersecting degs and tme-related genes, 3985 overlapping tme-related degs were selected for non-negative matrix factorization clustering, microenvironment cell populations-counter (mcp-counter), lasso cox regression, tumor immune dysfunction, and exclusion (tide) algorithm analyses. |
2024-01-30 |
2024-02-01 |
Not clear |
| Hyemi Lee, Jiho Nam, Hahyeong Jang, Young-Sik Park, Min-Hee Son, In-Hyun Lee, Seong-Il Eyun, Jimin Jeon, Siyoung Yan. Novel molecule BBC0901 inhibits BRD4 and acts as a catabolic regulator in the pathogenesis of osteoarthritis. Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie. vol 166. 2023-09-04. PMID:37666177. |
rna sequencing analysis of gene expression patterns showed that bbc0901 inhibited the expression of catabolic factors, such as matrix metalloproteinases (mmps) and cyclooxygenase (cox)2, along with reactive oxygen species (ros) production. |
2023-09-04 |
2023-09-07 |
mouse |
| Libo Wang, Deshuang Fu, Siyuan Weng, Hui Xu, Long Liu, Chunguang Guo, Yuqing Ren, Zaoqu Liu, Xinwei Ha. Genome-scale CRISPR-Cas9 screening stratifies pancreatic cancer with distinct outcomes and immunotherapeutic efficacy. Cellular signalling. 2023-07-19. PMID:37468054. |
in this study, using the 105 prognostic cancer essential genes identified by genome-scale crispr-cas9 screening and univariate cox analysis, we established and verified three heterogeneous subtypes via non-negative matrix factorization (nmf) and nearest template prediction (ntp) algorithms in the tcga-paad cohort (176 samples) and four multi-center cohorts (233 samples), respectively. |
2023-07-19 |
2023-08-14 |
Not clear |
| Wenhui Bai, Li Cheng, Liangkun Xiong, Maoming Wang, Hao Liu, Kaihuan Yu, Weixing Wan. Protein succinylation associated with the progress of hepatocellular carcinoma. Journal of cellular and molecular medicine. 2022-10-29. PMID:36308411. |
statistical methods were employed to analyse the data, including the non-negative matrix factorization (nmf) algorithm, t-distributed stochastic neighbour embedding (t-sne) algorithm, and cox regression analysis. |
2022-10-29 |
2023-08-14 |
Not clear |
| Bo Tang, Lanlin Hu, Tao Jiang, Yunchang Li, Huasheng Xu, Hang Zhou, Mei Lan, Ke Xu, Jun Yin, Chunxia Su, Caicun Zhou, Chuan X. A Metabolism-Related Gene Prognostic Index for Prediction of Response to Immunotherapy in Lung Adenocarcinoma. International journal of molecular sciences. vol 23. issue 20. 2022-10-27. PMID:36293001. |
we constructed a prognostic model as metabolism-related gene (mrg) of four genes by using weighted gene co-expression network analysis (wgcna), the nonnegative matrix factorization (nmf), and cox regression analysis of a luad dataset ( |
2022-10-27 |
2023-08-14 |
Not clear |
| Nanxing Yi, Yilin Mi, Xiaotong Xu, Naping Li, Baiyi Chen, Ke Yan, Kaiyun Tan, Bo Zhang, Linhua Wang, Gaoyan Kuang, Min L. Nodakenin attenuates cartilage degradation and inflammatory responses in a mice model of knee osteoarthritis by regulating mitochondrial Drp1/ROS/NLRP3 axis. International immunopharmacology. vol 113. issue Pt A. 2022-10-27. PMID:36302323. |
moreover, nod inhibited the mrna levels of inflammatory cytokines (cox 2, il-1β, and tnf-α), nod-like receptor family pyrin domain-containing 3 (nlrp3) inflammasome, and matrix metalloproteinase 13 expression in activated chondrocytes. |
2022-10-27 |
2023-08-14 |
mouse |
| Shih-Yao Chen, I-Ming Jou, Po-Yen Ko, Kai-Lan Hsu, Wei-Ren Su, Li-Chieh Kuo, Pei-Yuan Lee, Chao-Liang Wu, Po-Ting W. Amelioration of experimental tendinopathy by lentiviral CD44 gene therapy targeting senescence-associated secretory phenotypes. Molecular therapy. Methods & clinical development. vol 26. 2022-07-18. PMID:35846572. |
cd44 overexpressed tenocyte transfectants exhibited reduced levels of il-6, matrix metalloproteinases (mmps), cyclooxygenase (cox)-2, p53, p21, p16, sa-β-gal, and phospho-nuclear factor (nf)-κb, whereas their collagen type i alpha 1 (col1a1) and tenomodulin (tnmd) levels were increased when compared with control transfectants under il-1β-stimulated conditions. |
2022-07-18 |
2023-08-14 |
human |
| Wataru Morozumi, Kota Aoshima, Satoshi Inagaki, Yuki Iwata, Yuya Takagi, Shinsuke Nakamura, Hideaki Hara, Masamitsu Shimazaw. Piezo1 activation induces fibronectin reduction and PGF2α secretion via arachidonic acid cascade. Experimental eye research. 2022-01-02. PMID:34973946. |
activation of piezo1 in htmc showed increased expression of matrix metalloproteinase-2 (mmp-2) and cyclooxygenase (cox)-2, and decreased fibronectin expression. |
2022-01-02 |
2023-08-13 |
mouse |
| Hu Song, Chengwei Ruan, Yixin Xu, Teng Xu, Ruizhi Fan, Tao Jiang, Meng Cao, Jun Son. Survival stratification for colorectal cancer via multi-omics integration using an autoencoder-based model. Experimental biology and medicine (Maywood, N.J.). 2021-12-14. PMID:34904882. |
the autoencoder-based strategy was compared to the principal component analysis (pca)-, t-distributed random neighbor embedded (t-sne)-, non-negative matrix factorization (nmf)-, or individual cox proportional hazards (cox-ph)-based strategies. |
2021-12-14 |
2023-08-13 |
Not clear |
| Dinesh G Goswami, Neha Mishra, Rama Kant, Chapla Agarwal, Claire R Croutch, Robert W Enzenauer, Mark J Petrash, Neera Tewari-Singh, Rajesh Agarwa. Pathophysiology and inflammatory biomarkers of sulfur mustard-induced corneal injury in rabbits. PloS one. vol 16. issue 10. 2021-11-30. PMID:34637469. |
in this study, detailed analyses of histopathological alterations in corneal structure, keratocytes, inflammatory cells, blood vessels, and expressions of cyclooxygenase (cox)-2, matrix metalloproteinase (mmp)-9, vascular endothelial growth factor (vegf), and cytokines were performed in new zealand white rabbits, in a time-dependent manner till 28 days, post longer durations (5 and 7 min) of ocular sm exposure to establish quantifiable endpoints of injury and healing. |
2021-11-30 |
2023-08-13 |
Not clear |
| Jianwu Hu, Caiyun Chen, Yuan Su, Jiao DU, Xin Qian, Yang Ji. Vascular endothelial growth factor promotes the expression of cyclooxygenase 2 and matrix metalloproteinases in Lewis lung carcinoma cells. Experimental and therapeutic medicine. vol 4. issue 6. 2021-10-21. PMID:23226772. |
cyclooxygenase (cox)-2, matrix metalloproteinase (mmp)2, mmp9 and wild-type (wt) p53 has been found to regulate the production of vegf. |
2021-10-21 |
2023-08-12 |
Not clear |
| Shino Shibata-Kobayashi, Hideomi Yamashita, Kae Okuma, Kenshiro Shiraishi, Hiroshi Igaki, Kuni Ohtomo, Keiichi Nakagaw. Correlation among 16 biological factors [p53, p21(waf1), MIB-1 (Ki-67), p16(INK4A), cyclin D1, E-cadherin, Bcl-2, TNF-α, NF-κB, TGF-β, MMP-7, COX-2, EGFR, HER2/neu, ER, and HIF-1α] and clinical outcomes following curative chemoradiation therapy in 10 patients with esophageal squamous cell carcinoma. Oncology letters. vol 5. issue 3. 2021-10-21. PMID:23426606. |
the immunohistochemical expression levels of p53, p21(waf1), molecular immunology borstel-1 (mib-1, ki-67), p16(ink4a), cyclin d1, e-cadherin, bcl-2, tumor necrosis factor (tnf)-α, nuclear factor (nf)-κb, transforming growth factor (tgf)-β, matrix metalloproteinase (mmp)-7, cyclooxygenase (cox)-2, epidermal growth factor receptor (egfr), human egfr type 2 (her2/neu), estrogen receptor (er) and hypoxia-inducible factor (hif)-1α were studied in 10 cases of escc treated with ccrt. |
2021-10-21 |
2023-08-12 |
human |
| Jian Huang, Tingni Sun, Zhiliang Ying, Yi Yu, Cun-Hui Zhan. ORACLE INEQUALITIES FOR THE LASSO IN THE COX MODEL. Annals of statistics. vol 41. issue 3. 2021-10-21. PMID:24086091. |
in the cox regression model, the hessian matrix is based on time-dependent covariates in censored risk sets, so that the compatibility and cone invertibility factors, and the restricted eigenvalue as well, are random variables even when they are evaluated for the hessian at the true regression coefficients. |
2021-10-21 |
2023-08-12 |
Not clear |
| Priscila Motta Janovits, Elbio Leiguez, Viviane Portas, Catarina Teixeir. A Metalloproteinase Induces an Inflammatory Response in Preadipocytes with the Activation of COX Signalling Pathways and Participation of Endogenous Phospholipases A Biomolecules. vol 11. issue 7. 2021-09-23. PMID:34206390. |
a metalloproteinase induces an inflammatory response in preadipocytes with the activation of cox signalling pathways and participation of endogenous phospholipases a matrix metalloproteinases (mmps) are proteolytic enzymes that have been associated with the pathogenesis of inflammatory diseases and obesity. |
2021-09-23 |
2023-08-13 |
Not clear |
| Qiang Zhang, Birgit Rudolph, Mira Choi, Friederike Bachmann, Danilo Schmidt, Michael Duerr, Marcel G Naik, Wiebke Duettmann, Eva Schrezenmeier, Manuel Mayrdorfer, Fabian Halleck, Kaiyin Wu, Klemens Budd. The relationship between proteinuria and allograft survival in patients with transplant glomerulopathy: a retrospective single-center cohort study. Transplant international : official journal of the European Society for Organ Transplantation. vol 34. issue 2. 2021-06-28. PMID:33205460. |
proteinuria was associated with graft loss in univariable cox regression [hazard ratio (hr) 1.25, 95% ci, 1.11-1.41, p < 0.001], and in multivariable analysis (adjusted hr 1.26, 95% ci 1.11-1.42, p < 0.001) independent of other risk factors including creatinine at biopsy, positive c4d, history of rejection, and banff lesion score mesangial matrix expansion. |
2021-06-28 |
2023-08-13 |
Not clear |
| Xiaozhou Yang, Brittany L Bonnett, Glenn A Spiering, Hannah D Cornell, Bradley J Gibbons, Robert B Moore, E Johan Foster, Amanda J Morri. Understanding the Mechanical Reinforcement of Metal-Organic Framework-Polymer Composites: The Effect of Aspect Ratio. ACS applied materials & interfaces. 2021-06-04. PMID:34086436. |
in contrast, the percolation model and the cox model were unable to adequately fit the data, indicating the mechanical reinforcement in our system mainly originated from efficient load transfer between particles and the matrix in the particle orienting direction. |
2021-06-04 |
2023-08-13 |
Not clear |