Stomach adenocarcinoma (STAD) is a common malignancy with high heterogeneity and a lack of highly precise treatment options. We downloaded the multiomics data of STAD patients in The Cancer Genome Atlas (TCGA)-STAD cohort, which included mRNA, microRNA, long non-coding RNA, somatic mutation, and DNA methylation data, from the sxdyc website. We synthesized the multiomics data of patients with STAD using 10 clustering methods, construct a consensus machine learning-driven signature (CMLS)-related prognostic models by combining 10 machine learning methods, and evaluated the prognosis models using the C-index. The prognostic relationship between CMLS and STAD was assessed using Kaplan-Meier curves, and the independent prognostic value of CMLS was determined by univariate and multivariate regression analyses. we also evaluated the immune characteristics, immunotherapy response, and drug sensitivity of different CMLS groups. The results of the multiomics analysis classified STAD into three subtypes, with CS1 resulting in the best survival outcome. In total, 10 hub genes (CES3, AHCYL2, APOD, EFEMP1, CYP1B1, ASPN, CPE, CLIP3, MAP1B, and DKK1) were screened and constructed the CMLS was significantly correlated with prognosis in patients with STAD and was an independent prognostic factor for patients with STAD. Using the CMLS risk score, all patients were divided into a high CMLS group and a low CMLS group. Patients in the low-CMLS group had better survival, more enriched immune cells, and higher tumor mutation load scores, suggesting better immunotherapy responsiveness and a possible "hot tumor" phenotype. Patients in the high-CMLS group had a significantly poorer prognosis and were less sensitive to immunotherapy but were likely to benefit more from chemotherapy and targeted therapy. In this study, 10 clustering methods and 10 machine learning methods were combined to analyze the multiomics of STAD, classify STAD into three subtypes, and constructed CMLS-related prognostic model features, which are important for accurate management and effective treatment of STAD.
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http://dx.doi.org/10.1038/s41598-025-87444-3 | DOI Listing |
BMC Chem
January 2025
Department of Pharmacy, Birla Institute of Technology and Science Pilani, Pilani Campus, Vidya Vihar, Pilani, Rajasthan, 333 031, India.
A large set of antimalarial molecules (N ~ 15k) was employed from ChEMBL to build a robust random forest (RF) model for the prediction of antiplasmodial activity. Rather than depending on high throughput screening (HTS) data, molecules tested at multiple doses against blood stages of Plasmodium falciparum were used for model development. The open-access and code-free KNIME platform was used to develop a workflow to train the model on 80% of data (N ~ 12k).
View Article and Find Full Text PDFBioData Min
January 2025
Department of Applied Mathematics and Statistics, The State University of New York, Korea, Incheon, South Korea.
Background: The treatment effects are heterogenous across patients due to the differences in their microbiomes, which in turn implies that we can enhance the treatment effect by manipulating the patient's microbiome profile. Then, the coadministration of microbiome-based dietary supplements/therapeutics along with the primary treatment has been the subject of intensive investigation. However, for this, we first need to comprehend which microbes help (or prevent) the treatment to cure the patient's disease.
View Article and Find Full Text PDFBMC Oral Health
January 2025
Department of Anaesthesiology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China.
Background: Postoperative fever (POF) is a common occurrence in patients undergoing major surgery, presenting challenges and burdens for both patients and surgeons yet. This study endeavors to examine the incidence, identify risk factors, and establish a machine learning-based predictive model for POF following surgery of oral cancer.
Methods: A total of seven hundred and twenty-seven consecutive patients undergoing radical resection of oral cancer were retrospectively investigated.
BMC Pregnancy Childbirth
January 2025
Jiaxing Maternity and Child Health Care Hospital, Jiaxing, Zhejiang, 314001, China.
Background: Intrahepatic cholestasis of pregnancy (ICP) is a liver disorder that occurs in the second and third trimesters of pregnancy and is associated with a significant risk of fetal complications, including premature birth and fetal death. In clinical practice, the diagnosis of ICP is predominantly based on the presence of pruritus in pregnant women and elevated serum total bile acid. However, this approach may result in missed or delayed diagnoses.
View Article and Find Full Text PDFBMC Nephrol
January 2025
Department of Nephrology-Dialysis-Transplantation, University of Liège, CHU Sart Tilman, Liège, Belgium.
Background: Creatinine-based estimated glomerular filtration rate (eGFR) equations are widely used in clinical practice but exhibit inherent limitations. On the other side, measuring GFR is time consuming and not available in routine clinical practice. We developed and validated machine learning models to assess the trustworthiness (i.
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