Gene-induced Multimodal Pre-training for Image-omic Classification

Histology analysis of the tumor micro-environment integrated with genomic assays is the gold standard for most cancers in modern medicine. This paper proposes a Gene-induced Multimodal Pre-training (GiMP) framework, which jointly incorporates genomics and Whole Slide Images (WSIs) for classification tasks. Our work aims at dealing with the main challenges of multi-modality image-omic classification w.r.t. (1) the patient-level feature extraction difficulties from gigapixel WSIs and tens of thousands of genes, and (2) effective fusion considering high-order relevance modeling. Concretely, we first propose a group multi-head self-attention gene encoder to capture global structured features in gene expression cohorts. We design a masked patch modeling paradigm (MPM) to capture the latent pathological characteristics of different tissues. The mask strategy is randomly masking a fixed-length contiguous subsequence of patch embeddings of a WSI. Finally, we combine the classification tokens of paired modalities and propose a triplet learning module to learn high-order relevance and discriminative patient-level information.After pre-training, a simple fine-tuning can be adopted to obtain the classification results. Experimental results on the TCGA dataset show the superiority of our network architectures and our pre-training framework, achieving 99.47% in accuracy for image-omic classification. The code is publicly available at https://github.com/huangwudiduan/GIMP

Study of Local Mineralized Intensity Using Rescaled Range Analysis and Lacunarity Analysis

In this paper, the gold grade series along drifts have been analyzed using two methods, rescaled range analysis and lacunarity analysis which are commonly used in nonlinear systems analysis. The aim of this study is to better understand the ore-forming processes and identify the local mineralized intensity and interactions that influence the spatial structure of gold element grade distribution, in the Dayingezhuang fault-controlled, disseminated-veinlet gold deposit in the Jiaodong gold province, eastern China. The result shows that the efficiency of two methods, in distinguishing between weakly mineralized, moderately mineralized and intensely mineralized of ore-forming area. It is obvious that the two parameters of both Hurst and lacunarity index in the weakly mineralized drifts are distinguished from those in the mineralized drifts, and the lower the index is, the more homogeneously distributed of the elements and the mineral intensity is relatively smaller. The methods used in this paper provide a relatively comprehensive description for local mineral intensity, offering an evidence for the identification of mineralization intensity and providing a guidance for further determination to the extent of deposit concentration and delineation of target mineralization zone

A New Non-Abelian Topological Phase of Cold Fermi Gases in Anisotropic and Spin-Dependent Optical Lattices

To realize non-Abelian s-wave topological superfluid (TS) of cold Fermi gases, generally a Zeeman magnetic field larger than superfluid pairing gap is necessary. In this paper we find that using an anisotropic and spin-dependent optical lattice (ASDOL) to trap gases, a new non-Abelian TS phase appears, in contrast to an isotropic and spin-independent optical lattice. A characteristic of this new non-Abelian TS is that Zeeman magnetic field can be smaller than the superfluid pairing gap. By self-consistently solving pairing gap equation and considering the competition against normal state and phase separation, this new phase is also stable. Thus an ASDOL supplies a convenient route to realize TS. We also investigate edge states and the effects of a harmonic trap potential

Proteomic dissection of LPS-inducible, PHF8-dependent secretome reveals novel roles of PHF8 in TLR4-induced acute inflammation and T cell proliferation

Endotoxin (LPS)-induced changes in histone lysine methylation contribute to the gene-specific transcription for control of inflammation. Still unidentified are the chromatin regulators that drive the transition from a transcriptional-repressive to a transcriptional-active chromatin state of pro-inflammatory genes. Here, using combined approaches to analyze LPS-induced changes in both gene-specific transcription and protein secretion to the extracellular compartment, we characterize novel functions of the lysine demethylase PHF8 as a pro-inflammatory, gene-specific chromatin regulator. First, in the LPS-induced, acute-inflamed macrophages, PHF8 knockdown led to both a reduction of pro-inflammatory factors and an increase in a transcriptional-repressive code (H3K9me2) written by the methyltransferase G9a. Through unbiased quantitative secretome screening we discovered that LPS induces the secretion of a cluster of PHF8-dependent, ‘tolerizable’ proteins that are related to diverse extracellular pathways/processes including those for the activation of adaptive immunity. Specifically, we determined that PHF8 promotes T-cell activation and proliferation, thus providing the first link between the epigenetic regulation of inflammation and adaptive immunity. Further, we found that, in the acute-inflamed macrophages, the acute-active PHF8 opposes the H3K9me1/2-writing activity of G9a to activate specific protein secretions that are suppressed by G9a in the endotoxin-tolerant cells, revealing the inflammatory-phenotypic chromatin drivers that regulate the gene-specific chromatin plasticity