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STMGraph: spatial-context-aware of transcriptomes via a dual-remasked dynamic graph attention model.

Brief Bioinform

November 2024

Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, No. 15 Shangxiadian Road, Cangshan District, Fuzhou 350002, China.

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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Whole-body PET imaging is often hindered by respiratory motion during acquisition, causing significant degradation in the quality of reconstructed activity images. An additional challenge in PET/CT imaging arises from the respiratory phase mismatch between CT-based attenuation correction and PET acquisition, leading to attenuation artifacts. To address these issues, we propose two new, purely data-driven methods for the joint estimation of activity, attenuation, and motion in respiratory self-gated TOF PET.

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Introduction: The polyspermy rate is a quality control indicator in the embryology laboratory, and factors affecting polyspermy are of great interest. The gonadotropin-releasing hormone (GnRH) antagonist protocol is currently the mainstream protocol in most reproductive centers. This study explored the factors influencing polyspermy in fertilization (IVF) using the GnRH antagonist protocol and considered corresponding improvement measures.

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It is well known that activation of NMDA receptors can trigger long-term synaptic depression (LTD) and that a morphological correlate of this functional plasticity is spine retraction and elimination. Recent studies have led to the surprising conclusion that NMDA-induced spine shrinkage proceeds independently of ion flux and requires the initiation of protein synthesis, highlighting an unappreciated contribution of mRNA translation to non-ionotropic NMDAR signaling. Here we used NMDA-induced spine shrinkage in slices of mouse hippocampus as a readout to investigate this novel modality of synaptic transmission.

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Connections 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.

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