The COVID-19 pandemic, caused by the novel coronavirus SARS-CoV-2, creates an urgent need for identifying molecular mechanisms that mediate viral entry, propagation, and tissue pathology. Cell membrane bound angiotensin-converting enzyme 2 (ACE2) and associated proteases, transmembrane protease serine 2 (TMPRSS2) and Cathepsin L (CTSL), were previously identified as mediators of SARS-CoV2 cellular entry. Here, we assess the cell type-specific RNA expression of ACE2, TMPRSS2, and CTSL through an integrated analysis of 107 single-cell and single-nucleus RNA-Seq studies, including 22 lung and airways datasets (16 unpublished), and 85 datasets from other diverse organs. Joint expression of ACE2 and the accessory proteases identifies specific subsets of respiratory epithelial cells as putative targets of viral infection in the nasal passages, airways, and alveoli. Cells that co-express ACE2 and proteases are also identified in cells from other organs, some of which have been associated with COVID-19 transmission or pathology, including gut enterocytes, corneal epithelial cells, cardiomyocytes, heart pericytes, olfactory sustentacular cells, and renal epithelial cells. Performing the first meta-analyses of scRNA-seq studies, we analyzed 1,176,683 cells from 282 nasal, airway, and lung parenchyma samples from 164 donors spanning fetal, childhood, adult, and elderly age groups, associate increased levels of ACE2, TMPRSS2, and CTSL in specific cell types with increasing age, male gender, and smoking, all of which are epidemiologically linked to COVID-19 susceptibility and outcomes. Notably, there was a particularly low expression of ACE2 in the few young pediatric samples in the analysis. Further analysis reveals a gene expression program shared by ACE2 + TMPRSS2 + cells in nasal, lung and gut tissues, including genes that may mediate viral entry, subtend key immune functions, and mediate epithelial-macrophage cross-talk. Amongst these are IL6, its receptor and co-receptor, IL1R, TNF response pathways, and complement genes. Cell type specificity in the lung and airways and smoking effects were conserved in mice. Our analyses suggest that differences in the cell type-specific expression of mediators of SARS-CoV-2 viral entry may be responsible for aspects of COVID-19 epidemiology and clinical course, and point to putative molecular pathways involved in disease susceptibility and pathogenesis.

Angiotensin-converting enzyme 2 (ACE2) and accessory proteases (TMPRSS2 and CTSL) are needed for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) cellular entry, and their expression may shed light on viral tropism and impact across the body. We assessed the cell-type-specific expression of ACE2, TMPRSS2 and CTSL across 107 single-cell RNA-sequencing studies from different tissues. ACE2, TMPRSS2 and CTSL are coexpressed in specific subsets of respiratory epithelial cells in the nasal passages, airways and alveoli, and in cells from other organs associated with coronavirus disease 2019 (COVID-19) transmission or pathology. We performed a meta-analysis of 31 lung single-cell RNA-sequencing studies with 1,320,896 cells from 377 nasal, airway and lung parenchyma samples from 228 individuals. This revealed cell-type-specific associations of age, sex and smoking with expression levels of ACE2, TMPRSS2 and CTSL. Expression of entry factors increased with age and in males, including in airway secretory cells and alveolar type 2 cells. Expression programs shared by ACE2 + TMPRSS2 + cells in nasal, lung and gut tissues included genes that may mediate viral entry, key immune functions and epithelial-macrophage cross-talk, such as genes involved in the interleukin-6, interleukin-1, tumor necrosis factor and complement pathways. Cell-type-specific expression patterns may contribute to the pathogenesis of COVID-19, and our work highlights putative molecular pathways for therapeutic intervention.

Particle swarm optimization (PSO), an intelligent optimization algorithm inspired by the flocking behavior of birds, has been shown to perform well and widely used to solve the continuous problem. But the traditional PSO and most of its variants are developed for optimization problems in continuous space, which are not able to solve the binary combinational optimization problem. To tackle this problem, Kennedy extended the PSO and proposed a discrete binary PSO. But its performance is not ideal and just few further works were conducted based on it. In this paper, we propose a novel probability binary particle swarm optimization (PBPSO) algorithm for discrete binary optimization problems. In PBPSO, a novel updating strategy is adopted to update the swarm and search the global solution, which further simplify the computations and improve the optimization ability. To investigate the performance of the proposed PBPSO, the multidimensional knapsack problems are used as the test benchmarks. The experimental results demonstrate that PBPSO has a better performance for solving the multidimensional knapsack problem in terms of convergent speed and global search ability.

Target-enabled bioorthogonal reaction and self-assembly of a small-molecule probe into supramolecules have shown promise for molecular imaging. In this paper, we report a new stimuli-responsive bioorthogonal reaction scaffold (SF) for controlling in situ self-assembly by engineering the condensation reaction between 2-cyanobenzothiazole and cysteine. For probes with the SF scaffold, intramolecular cyclization took place soon after activation, which could efficiently outcompete free cysteine even at a low concentration and result in efficient aggregation in the target. Through integration with different enzyme-responsive substrates and an ammoniomethyl-trifluoroborate moiety (AmBF3), two radioactive positron emission tomography (PET) tracers, [18F]SF-DEVD and [18F]SF-Glu, were designed, which showed high stability under physiological conditions and could produce clear PET signal in tumors to detect enzyme activity (e.g., caspase-3, γ-glutamyltranspeptidase) timely and accurately. Our results demonstrated that the scaffold SF could serve as a general molecular scaffold in the development of smart PET tracers for noninvasive imaging of enzyme activity, which could contribute to tumor detection and treatment efficacy evaluation.

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Legumain has been found overexpressed in several cancers, which serves as an important biomarker for cancer diagnosis. In this research, a novel fluorine-18 labeled radioactive tracer [18F]SF-AAN targeting legumain was designed and synthesized for positron emission tomography (PET) imaging. Nonradioactive probe [19F]SF-AAN was obtained through chemical and solid phase peptide synthesis. After a simple one-step 18F labeling, the radiotracer [18F]SF-AAN was obtained with a high radiochemical conversion rate (>85%) and radiochemical purity (99%) as well as high molar activity (12.77 ± 0.50 MBq/nmol). The targeting specificity of [18F]SF-AAN for detecting legumain activity was investigated systematically in vitro and in vivo. In vitro cellular uptake assay showed that the uptake of [18F]SF-AAN in legumain-positive MDA-MB-468 cells was twice as much as that in legumain-negative PC-3 cells at 4 h. In vivo PET imaging revealed that the tumor uptake of [18F]SF-AAN in MDA-MB-468 tumor-bearing mice was about 2.7 times of that in PC-3 tumor-bearing mice at 10 min post injection. The experimental results indicated that [18F]SF-AAN could serve as a promising PET tracer for detecting the legumain expression sensitively and specifically, which would be beneficial for the diagnosis of legumain-related diseases.

A series of flow experiments were performed on matched fractures to study the problem of non-Darcy flow in fractured media. Five rock fractures of different roughness were generated using indirect tensile tests, and their surface topographies were measured using a stereo topometric scanning system. The fracture was assumed to be a self-affine surface, and its roughness and anisotropy were quantified by the fractal dimension. According to the flow tortuosity effect, the nonlinear flow was characterized by hydraulic tortuosity and surface tortuosity power law relationships based on Forchheimer’s law. Fracture seepage experiments conducted with two injection directions (0° and 90°) showed that Forchheimer’s law described the nonlinear flow well. Both the proposed model and Chen’s double-parameter model gave similar results to the experiment, but the match was closer with the proposed model. On this basis, a new formula for the critical Reynolds number is proposed, which serves to distinguish linear flow and Forchheimer flow.

Poor fiber orientation and mismatched bone-ligament interface fusion have plagued the regeneration of periodontal defects by cell-based scaffolds. A 3D bioprinted biomimetic periodontal module is designed with high architectural integrity using a methacrylate gelatin/decellularized extracellular matrix (GelMA/dECM) cell-laden bioink. The module presents favorable mechanical properties and orientation guidance by high-precision topographical cues and provides a biochemical environment conducive to regulating encapsulated cell behavior. The dECM features robust immunomodulatory activity, reducing the release of proinflammatory factors by M1 macrophages and decreasing local inflammation in Sprague Dawley rats. In a clinically relevant critical-size periodontal defect model, the bioprinted module significantly enhances the regeneration of hybrid periodontal tissues in beagles, especially the anchoring structures of the bone-ligament interface, well-aligned periodontal fibers, and highly mineralized alveolar bone. This demonstrates the effectiveness and feasibility of 3D bioprinting combined with a dental follicle-specific dECM bioink for periodontium regeneration, providing new avenues for future clinical practice.