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Protocol to boost the robustness and accuracy of spatial transcriptomics algorithms using ensemble techniques.
STAR Protoc
January 2025
Department of Statistics, University of Georgia, 310 Herty Drive, Athens, GA 30602, USA. Electronic address:
Spatial transcriptomics enhances our understanding of cellular organization by mapping gene expression data to precise tissue locations. Here, we present a protocol for using weighted ensemble method for spatial transcriptomics (WEST), which uses ensemble techniques to boost the robustness and accuracy of existing algorithms. We describe steps for preprocessing data, obtaining embeddings from individual algorithms, and ensemble integrating all embeddings as a similarity matrix.
View Article and Find Full Text PDFThe spatial arrangement of cells plays a pivotal role in shaping tissue functions in various biological systems and diseased microenvironments. However, it is still under-investigated of the topological coordinating rules among different cell types as tissue spatial patterns. Here, we introduce the Triangulation cellular community motif Neural Network (TrimNN), a bottom-up approach to estimate the prevalence of sizeable conservative cell organization patterns as Cellular Community (CC) motifs in spatial transcriptomics and proteomics.
View Article and Find Full Text PDFVisualization of pure phase objects with optical spatial differentiation operations.
Opt Express
January 2025
Phase distributions typically contain richer information about the morphology, structure, and organizational properties of a sample than intensity distributions. However, due to the weak scattering and absorption properties of pure phase objects, intensity measurements are unable to provide information about the phase, making it more challenging to reveal phase structure from the incident light background. Here, we propose a method for visualizing phase objects through simple optical reflection occurring at a glass interface.
View Article and Find Full Text PDFReference genome provide insights into sex determination of silver aworana (Osteoglossum bicirrhosum).
BMC Biol
January 2025
Key Laboratory of Prevention and Control for Aquatic Invasive Alien Species, Ministry of Agriculture and Rural Affairs, Guangdong Modern Recreational Fisheries Engineering Technology Center, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China.
Background: Silver arowana (Osteoglossum bicirrhosum) is a basal fish species with sexual monomorphism, while its sex determination mechanism has been poorly understood, posing a significant challenge to its captive breeding efforts.
Results: We constructed two high-quality chromosome-level genome assemblies for both female and male silver arowana, with scaffold N50 values over 10 Mb. Combining re-sequencing data of 109 individuals, we identified a female-specific region, which was localized in a non-coding region, i.
Deepening water scarcity in breadbasket nations.
Nat Commun
January 2025
Department of Geography and Spatial Sciences, University of Delaware, Newark, DE, USA.
Water is crucial for meeting sustainability targets, but its unsustainable use threatens human wellbeing and the environment. Past assessments of water scarcity (i.e.
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