Network-based analysis revealed significant interactions between risk genes of severe COVID-19 and host genes interacted with SARS-CoV-2 proteins.

Whether risk genes of severe coronavirus disease 2019 (COVID-19) from genome-wide association study could play their regulatory roles by interacting with host genes that were interacted with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) proteins was worthy of exploration. In this study, we implemented a network-based approach by developing a user-friendly software Network Calculator (https://github.com/Haoxiang-Qi/Network-Calculator.git). By using Network Calculator, we identified a network composed of 13 risk genes and 28 SARS-CoV-2 interacted host genes that had the highest network proximity with each other, with a hub gene HNRNPK identified. Among these genes, 14 of them were identified to be differentially expressed in RNA-seq data from severe COVID-19 cases. Besides, by expression enrichment analysis in single-cell RNA-seq data, compared with mild COVID-19, these genes were significantly enriched in macrophage, T cell and epithelial cell for severe COVID-19. Meanwhile, 74 pathways were significantly enriched. Our analysis provided insights for the underlying genetic etiology of severe COVID-19 from the perspective of network biology.

Identifying the twist factor of twisted partially coherent optical beams.

Twisted partially coherent light, characterized by its unique twist factor, offers novel control over the statistical properties of random light. However, the recognition of the twist factor remains a challenge due to the low coherence and the stochastic nature of the optical beam. This paper introduces a method for the recognition of twisted partially coherent beams by utilizing a circular aperture at the source plane. This aperture produces a characteristic hollow intensity structure due to the twist phase. A deep learning model is then trained to identify the twist factor of these beams based on this signature. The model, while simple in structure, effectively eliminates the need for complex optimization layers, streamlining the recognition process. This approach offers a promising solution for enhancing the detection of twisted light and paves the way for future research in this field.

Partially coherent twisted vector vortex beam enabling manipulation of high-dimensional classical entanglement.

In this paper, we present a novel form of a partially coherent beam characterized by classical entanglement in higher dimensions. We coin the term "twisted vector vortex (TVV) beam" to describe this phenomenon. Similar to multi-partite quantum entangled states in higher dimensions, the partially coherent twisted vector vortex beam possesses distinct properties such as non-uniform polarization, vortex phase, and twist phase. Through experiments, we offer empirical evidence for these three degrees-of-freedom in the light field. The results demonstrate that the state of the light is inseparable in terms of polarization and orbital angular momentum (OAM) modes. Additionally, the twist phase introduces an additional dimension in controlling the vector vortex beam. This research reveals the possibility of new controlling dimensions in classical entanglement through the chirality of coherence within partially coherent light. Consequently, this opens up new avenues for the utilization of partially coherent light in both classical and quantum domains.

Generating a hollow twisted correlated beam using correlated perturbations.

In this study, a twisted correlated optical beam with a dark hollow center in its average intensity is synthesized by correlated correlation perturbation and incoherent mode superposition. This new hollow beam has a topological charge (TC) mode with a zero value compared with a coherence vortex that has a TC mode with a nonzero value. We transform the twisted correlated beam from solid centered to dark hollow centered by constructing a correlation between the twist factor and the spot structure parameter. Theoretical and experimental results show that twist correlation makes the random optical beam an asymmetric orbital angular momentum spectral distribution and a tunable intensity center. Controlling the correlation parameters can make the focal spot of the twisted beam a dark core when the dominant mode of the TC is still zero. The new nontrivial beams and their proposed generation method provide important technical preparations for the optical particle manipulation with low coherence environment.