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scSMD: a deep learning method for accurate clustering of single cells based on auto-encoder.
BMC Bioinformatics
January 2025
Department of Surgery, Shanghai Key Laboratory of Gastric Neoplasms, Shanghai Institute of Digestive Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
Background: Single-cell RNA sequencing (scRNA-seq) has transformed biological research by offering new insights into cellular heterogeneity, developmental processes, and disease mechanisms. As scRNA-seq technology advances, its role in modern biology has become increasingly vital. This study explores the application of deep learning to single-cell data clustering, with a particular focus on managing sparse, high-dimensional data.
View Article and Find Full Text PDFiRGD-Targeted Biosynthetic Nanobubbles for Ultrasound Molecular Imaging of Osteosarcoma.
Int J Nanomedicine
January 2025
Department of Ultrasound, The second People's Hospital of Shenzhen, The First Affiliated Hospital of Shenzhen University, Shenzhen, 518061, People's Republic of China.
Purpose: Osteosarcoma is the most common primary malignant tumor of the bone. However, there is a lack of effective means for early diagnosis due to the heterogeneity of tumors and the complexity of tumor microenvironment. αvβ3 integrin, a crucial role in the growth and spread of tumors, is not only an effective biomarker for cancer angiogenesis, but also highly expressed in many tumor cells.
View Article and Find Full Text PDFClassification of Fibro-osseous Tumors in the Craniofacial Bones using DNA Methylation and Copy Number Alterations.
Mod Pathol
January 2025
Department of Pathology and Medical Biology, University Medical Center Groningen, Groningen, the Netherlands; Department of Pathology, Amsterdam University Medical Center, Amsterdam, the Netherlands. Electronic address:
Fibro-osseous tumors of the craniofacial bones are a heterogeneous group of lesions comprising cemento-osseous dysplasia (COD), cemento-ossifying fibroma (COF), juvenile trabecular ossifying fibroma (JTOF), psammomatoid ossifying fibroma (PsOF), fibrous dysplasia (FD), and low-grade osteosarcoma (LGOS) with overlapping clinicopathological features. However, their clinical behavior and treatment differ significantly, underlining the need for accurate diagnosis. Molecular diagnostic markers exist for subsets of these tumors, including GNAS mutations in FD, SATB2 fusions in PsOF, mutations involving the RAS-MAPK signaling pathway in COD, and MDM2 amplification in LGOS.
View Article and Find Full Text PDFTransketolase promotes osteosarcoma progression through the YY1-PAK4 axis.
FEBS J
January 2025
Department of Orthopedics, Wuhan Hospital of Traditional Chinese and Western Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
Osteosarcoma, a malignant bone tumor that occurs in adolescents, proliferates and is prone to pulmonary metastasis. Osteosarcoma is characterized by high genotypic heterogeneity, making it difficult to identify reliable anti-osteosarcoma targets. The genotype of osteosarcoma may be highly dynamic, but its high dependence on energy remains constant.
View Article and Find Full Text PDFOngoing chromothripsis underpins osteosarcoma genome complexity and clonal evolution.
Cell
January 2025
European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton CB10 1SA, UK. Electronic address:
Osteosarcoma is the most common primary cancer of the bone, with a peak incidence in children and young adults. Using multi-region whole-genome sequencing, we find that chromothripsis is an ongoing mutational process, occurring subclonally in 74% of osteosarcomas. Chromothripsis generates highly unstable derivative chromosomes, the ongoing evolution of which drives the acquisition of oncogenic mutations, clonal diversification, and intra-tumor heterogeneity across diverse sarcomas and carcinomas.
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