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| http://dx.doi.org/10.1186/s12964-024-01766-9 | DOI Listing |
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Horizontal Distortion Correction of AFM Images Based on Automatic Labeling of Feature Graphics.
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School of Electrical & Control Engineering, Shenyang Jianzhu University, Shenyang, China.
The atomic force microscope (AFM) image will be inclined and bent due to the tilt angle between the probe and the sample surface. When the least squares fitting method is used to correct the horizontal distortion of the AFM image, the shape structure that is lower or higher than the sample base will affect the final fitting correction result. In view of the limitations of existing methods and the diversity of AFM images, an AFM image level distortion correction method based on automatic feature marking is proposed.
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Spatial transcriptomics (ST) technologies enable dissecting the tissue architecture in spatial context. To perceive the global contextual information of gene expression patterns in tissue, the spatial dependence of cells must be fully considered by integrating both local and non-local features by means of spatial-context-aware. However, the current ST integration algorithm ignores for ST dropouts, which impedes the spatial-aware of ST features, resulting in challenges in the accuracy and robustness of microenvironmental heterogeneity detecting, spatial domain clustering, and batch-effects correction.
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View Article and Find Full Text PDFConnections between the mechanical properties of DNA and biological functions have been speculative due to the lack of methods to measure or predict DNA mechanics at scale. Recently, a proxy for DNA mechanics, cyclizability, was measured by loop-seq and enabled genome-scale investigation of DNA mechanics. Here, we use this dataset to build a computational model predicting bias-corrected intrinsic cyclizability, with near-perfect accuracy, solely based on DNA sequence.
View Article and Find Full Text PDFArticle Synopsis
- The use of well-structured ontologies and ontology-aware tools enhances data and analyses to be FAIR (Findable, Accessible, Interoperable, Reusable), supporting effective lexical searches and biologically meaningful annotation grouping.
- Researchers face challenges in adopting ontologies, primarily due to their complexity and the tendency to create simplified hierarchies that may misuse relationship types, leading to ineffective organization.
- A suite of validation tools is introduced to help users align their hierarchies with established ontology structures, providing graphical reports and tailored views for various atlases like the HuBMAP Human Reference Atlas and the Human Developmental Cell Atlas.
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