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CSI-GEP: A GPU-based unsupervised machine learning approach for recovering gene expression programs in atlas-scale single-cell RNA-seq data.
Cell Genom
January 2025
Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA. Electronic address:
Exploratory analysis of single-cell RNA sequencing (scRNA-seq) typically relies on hard clustering over two-dimensional projections like uniform manifold approximation and projection (UMAP). However, such methods can severely distort the data and have many arbitrary parameter choices. Methods that can model scRNA-seq data as non-discrete "gene expression programs" (GEPs) can better preserve the data's structure, but currently, they are often not scalable, not consistent across repeated runs, and lack an established method for choosing key parameters.
View Article and Find Full Text PDFA Global Collaborative Comparison of SARS-CoV-2 Antigenicity Across 15 Laboratories.
Viruses
December 2024
World Health Organization, 1202 Geneva, Switzerland.
Setting up a global SARS-CoV-2 surveillance system requires an understanding of how virus isolation and propagation practices, use of animal or human sera, and different neutralisation assay platforms influence assessment of SARS-CoV-2 antigenicity. In this study, with the contribution of 15 independent laboratories across all WHO regions, we carried out a controlled analysis of neutralisation assay platforms using the first WHO International Standard for antibodies to SARS-CoV-2 variants of concern (source: NIBSC). Live virus isolates (source: WHO BioHub or individual labs) or spike plasmids (individual labs) for pseudovirus production were used to perform neutralisation assays using the same serum panels.
View Article and Find Full Text PDFBufadienolides from Chansu Injection Synergistically Enhances the Antitumor Effect of Erlotinib by Inhibiting the KRAS Pathway in Pancreatic Cancer.
Pharmaceuticals (Basel)
December 2024
Key Laboratory of Xinjiang Endemic and Ethnic Diseases, Ministry of Education, Shihezi University School of Medicine, Shihezi 832003, China.
The Chansu injection (CSI), a sterile aqueous solution derived from Chansu, is applied in clinical settings to support antitumor and anti-radiation treatments. CSI's principal active components, bufadienolides (≥90%), demonstrate potential effects on pancreatic cancer (PDAC), but their underlying mechanisms remain unclear. This study aimed to elucidate the antitumor effects and pathways associated with CSI in PDAC.
View Article and Find Full Text PDFFam102a translocates Runx2 and Rbpjl to facilitate Osterix expression and bone formation.
Nat Commun
January 2025
Faculty of Dentistry, Institute of Science Tokyo, Tokyo, Japan.
Bone remodeling maintains the robustness of the bone tissue by balancing bone resorption by osteoclasts and bone formation by osteoblasts. Although these cells together play a crucial role in bone remodeling, only a few reports are available on the common factors involved in the differentiation of the two types of cells. Here, we show family with sequence similarity 102 member A (Fam102a) as a bone-remodeling factor that positively regulates both osteoclast and osteoblast differentiation.
View Article and Find Full Text PDFCorrelation of Two-Minute and Six-Minute Walk Tests With Spirometric Indices in Patients With Severe Chronic Obstructive Pulmonary Disease at a Selected Tertiary Care Hospital in Puducherry.
Cureus
November 2024
Pulmonary Medicine, Sri Manakula Vinayagar Medical College and Hospital, Puducherry, IND.
Background Chronic obstructive pulmonary disease (COPD) is a progressive respiratory condition characterised by airflow limitation and reduced exercise capacity. The Six-Minute Walk Test (6MWT) and Two-Minute Walk Test (2MWT) are commonly used to assess functional exercise capacity in COPD patients. This study aims to evaluate the correlation between the distance covered in the 2MWT and 6MWT with spirometric indices (such as Forced Expiratory Volume in 1 second (FEV₁), Forced Vital Capacity (FVC), and FEV₁/FVC) in COPD patients.
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