Browsing by Author "Kang, Jian"

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    SPARTIN: a Bayesian method for the quantification and characterization of cell type interactions in spatial pathology data
    (Frontiers Media S.A., 2023) Osher, Nathaniel; Kang, Jian; Krishnan, Santhoshi; Rao, Arvind; Baladandayuthapani, Veerabhadran
    Introduction: The acquisition of high-resolution digital pathology imaging data has sparked the development of methods to extract context-specific features from such complex data. In the context of cancer, this has led to increased exploration of the tumor microenvironment with respect to the presence and spatial composition of immune cells. Spatial statistical modeling of the immune microenvironment may yield insights into the role played by the immune system in the natural development of cancer as well as downstream therapeutic interventions.Methods: In this paper, we present SPatial Analysis of paRtitioned Tumor-Immune imagiNg (SPARTIN), a Bayesian method for the spatial quantification of immune cell infiltration from pathology images. SPARTIN uses Bayesian point processes to characterize a novel measure of local tumor-immune cell interaction, Cell Type Interaction Probability (CTIP). CTIP allows rigorous incorporation of uncertainty and is highly interpretable, both within and across biopsies, and can be used to assess associations with genomic and clinical features.Results: Through simulations, we show SPARTIN can accurately distinguish various patterns of cellular interactions as compared to existing methods. Using SPARTIN, we characterized the local spatial immune cell infiltration within and across 335 melanoma biopsies and evaluated their association with genomic, phenotypic, and clinical outcomes. We found that CTIP was significantly (negatively) associated with deconvolved immune cell prevalence scores including CD8+ T-Cells and Natural Killer cells. Furthermore, average CTIP scores differed significantly across previously established transcriptomic classes and significantly associated with survival outcomes.Discussion: SPARTIN provides a general framework for investigating spatial cellular interactions in high-resolution digital histopathology imaging data and its associations with patient level characteristics. The results of our analysis have potential implications relevant to both treatment and prognosis in the context of Skin Cutaneous Melanoma. The R-package for SPARTIN is available at https://github.com/bayesrx/SPARTIN along with a visualization tool for the images and results at: https://nateosher.github.io/SPARTIN.
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    Spin anisotropy due to spin-orbit coupling in optimally hole-doped Ba0:67K0:33Fe2As2
    (American Physical Society, 2016) Song, Yu; Man, Haoran; Zhang, Rui; Lu, Xingye; Zhang, Chenglin; Wang, Meng; Tan, Guotai; Regnault, L.-P.; Su, Yixi; Kang, Jian; Fernandes, Rafael M.; Dai, Pengcheng
    We use polarized inelastic neutron scattering to study the temperature and energy dependence of spin space anisotropies in the optimally-hole-doped iron pnictide Ba0.67K0.33Fe2As2 (Tc=38 K). In the superconducting state, while the high-energy part of the magnetic spectrum is nearly isotropic, the low-energy part displays a pronounced anisotropy, manifested by a c-axis polarized resonance. We also observe that the spin anisotropy in superconducting Ba0.67K0.33Fe2As2 extends to higher energies compared with electron-doped BaFe2−xTMxAs2 (TM=Co, Ni) and isovalent-doped BaFe2As1.4P0.6, suggesting a connection between Tc and the energy scale of the spin anisotropy. In the normal state, the low-energy spin anisotropy for hole- and electron-doped iron pnictides near optimal superconductivity onset at temperatures similar to the temperatures at which the elastoresistance deviates from Curie–Weiss behavior, pointing to a possible connection between the two phenomena. Our results highlight the relevance of the spin-orbit coupling to the superconductivity of the iron pnictides.