Bioinformatics analyses of gene expression profile to identify pathogenic mechanisms for COVID-19 infection and cutaneous lupus erythematosus

ObjectiveThe global mortality rates have surged due to the ongoing coronavirus disease 2019 (COVID-19), leading to a worldwide catastrophe. Increasing incidents of patients suffering from cutaneous lupus erythematosus (CLE) exacerbations after either contracting COVID-19 or getting immunized against it, have been observed in recent research. However, the precise intricacies that prompt this unexpected complication are yet to be fully elucidated. This investigation seeks to probe into the molecular events inciting this adverse outcome.MethodGene expression patterns from the Gene Expression Omnibus (GEO) database, specifically GSE171110 and GSE109248, were extracted. We then discovered common differentially expressed genes (DEGs) in both COVID-19 and CLE. This led to the creation of functional annotations, formation of a protein-protein interaction (PPI) network, and identification of key genes. Furthermore, regulatory networks relating to these shared DEGs and significant genes were constructed.ResultWe identified 214 overlapping DEGs in both COVID-19 and CLE datasets. The following functional enrichment analysis of these DEGs highlighted a significant enrichment in pathways related to virus response and infectious disease in both conditions. Next, a PPI network was constructed using bioinformatics tools, resulting in the identification of 5 hub genes. Finally, essential regulatory networks including transcription factor-gene and miRNA-gene interactions were determined.ConclusionOur findings demonstrate shared pathogenesis between COVID-19 and CLE, offering potential insights for future mechanistic investigations. And the identification of common pathways and key genes in these conditions may provide novel avenues for research

Submicron structure random field on granular soil material with retinex algorithm optimization

In this paper, a Retinex scale optimized image enhancement algorithm is proposed, which can enhance the micro vision image and eliminate the influence of the uneven illumination. Based on that, a random geometric model of the microstructure of granular materials is established with Monte-Carlo method, the numerical simulation including consolidation process of granular materials is compared with the experimental data. The results have proved that the random field method with Retinex image enhancement algorithm is effective, the image of microstructure of granular materials becomes clear and the contrast ratio is improved, after using Retinex image enhancement algorithm to enhance the CT image. The fidelity of enhanced image is higher than that dealing with other method, which have explained that the algorithm can preserve the microstructure information of the image well. The result of numerical simulation is similar with the one obtained from conventional three axis consolidation test, which proves that the simulation result is reliable

Calculation of Soil Deformation Caused by Shield Tunneling through the Sludge Layer with Plastic Drainage Plates

Due to a lack of engineering experience, research on ground deformation during shield machine tunneling in sludge layers is limited, especially in areas with plastic drainage plates installed for ground stabilization. When the shield passes through this area, the shield cutterhead may be jammed by the drainage plates, resulting in excavation surface instability, excess ground deformation, and schedule delay. In this work, a Mindlin solution for ground deformation in such a layer is obtained, considering four factors: the frontal additional pressure generated by the shield cutterhead due to the soil squeezing effect, the uneven lateral friction between the shield shell and the soil, the frontal friction generated by the shield cutterhead when cutting through the drainage plate, and the shield machine restart after shutdown. The results show that the theoretical curve is in good agreement with the measured values. The maximum settlement was approximately 10 m behind the excavation surface, and the maximum uplift was approximately 5 m in front of the excavation surface. The most influential factor among all the studied factors was the additional pressure on the shield cutter, which accounted for approximately 56% of the maximum settlement and 60% of the maximum uplift. The soil settlement mainly occurred within 12 m on both sides of the tunnel axis. The maximum settlements at the different soil depths tested were all directly below the tunnel axis

Anisotropic Bounding Surface Plasticity Model for Porous Media

An anisotropic plasticity model for the description of nonisotropic mechanical behaviors of porous media is presented. This model is developed using bounding surface plasticity theory within the critical state framework. The inherent and stress-induced anisotropy has been accounted for by an anisotropic variable, which is employed with the consideration of both irrecoverable deformation and stress state. The evolution of anisotropy has been described by both rotational and distortional hardening rules. The rotational hardening rule is proposed for the consideration of bounding surface inclination induced by inherent or induced anisotropy. The distortional hardening rule is developed to capture the varying shape of bounding surface associated with the accumulation of irrecoverable deformation and anisotropy. This model has been validated through modeling the stress–strain responses of porous media under various loading conditions, including triaxial drained/undrained compression/extension tests on both isotropically and anisotropically consolidated samples. Good agreement between model simulation and experimental results has been achieved for all cases taken into consideration, demonstrating the capability of the proposed model

Submicron structure random field on granular soil material with retinex algorithm optimization

In this paper, a Retinex scale optimized image enhancement algorithm is proposed, which can enhance the micro vision image and eliminate the influence of the uneven illumination. Based on that, a random geometric model of the microstructure of granular materials is established with Monte-Carlo method, the numerical simulation including consolidation process of granular materials is compared with the experimental data. The results have proved that the random field method with Retinex image enhancement algorithm is effective, the image of microstructure of granular materials becomes clear and the contrast ratio is improved, after using Retinex image enhancement algorithm to enhance the CT image. The fidelity of enhanced image is higher than that dealing with other method, which have explained that the algorithm can preserve the microstructure information of the image well. The result of numerical simulation is similar with the one obtained from conventional three axis consolidation test, which proves that the simulation result is reliable

A Unified Equation to Predict the Permeability of Rough Fractures via Lattice Boltzmann Simulation

In this paper, the fluid flow through rough fractures was investigated via numerical simulation based on the lattice Boltzmann method (LBM). The accuracy of LBM was validated through the numerical simulation of the parallel plate model and the verification of the mass conservation of fluid flow through rough fracture. After that, the effect of roughness on fluid flow was numerically conducted, in which, the geometry of fractures was characterized by the joint roughness coefficient (JRC), fractal dimension (D) and standard deviation (σ). It was found that the JRC cannot reflect the realistic influence of roughness on the permeability of single fracture, in which, an increase in permeability with increasing JRC has been observed at the range of 8~12 and 14~16. The reason behind this was revealed through the calculation of the root mean square of the first derivative of profile (Z2), and an equation has been proposed to estimate the permeability based on the aperture and Z2 of the fracture. The numerical simulations were further conducted on fluid flow though synthetic fractures with a wide range of D and σ. In order to unify the parameter that characterizes the roughness, Z2 was obtained for each synthetic fracture, and the corresponding relationship between permeability, aperture and Z2 was analyzed. Meanwhile, it was found that the fluid flow behaves differently with different ranges of Z2 and the critical point was found to be Z2 = 0.5. Based on extensive study, it was concluded that Z2 is a generic parameter characterizing the roughness, and the proposed equation could be used to predict the permeability for fluid flow in fracture

Spherical cavity expansion in porous rock considering plasticity and damage

In rock engineering, damage evolution upon loading imposes significant impacts on the stiffness of rock mass and its deformation characteristics. In order to investigate the influence of both damage and plasticity on cavity expansion, a plastic damage solution is derived for undrained spherical cavity expansion in rock medium. For the consideration of plasticity-damage, Modified Cam-Clay (MCC) model is selected as the plasticity driver, a damage evolution criterion is adopted and coupled with MCC. The coupled damage MCC model is validated against experimental data in the literature. The proposed cavity expansion solution with the consideration of plasticity damage is verified through a classic solution in literature. The role of damage in undrained spherical cavity expansion is investigated by studying the spatial variations of effective stress, pore pressure and damage for cases with different stress ratios. Distribution of cavity expansion induced plastic and damage zones for cases with different stress ratios are also reproduced and discussed. Cavity expansion results show that, the damage zone should be considered for engineering application as the plastic zone is affected due to the damage evolution. In addition, the stability (e.g., radial stress) of rock mass is overestimated in classical solution without the consideration of damage zone

Risk Analysis and Control Measures for Slurry Shield Tunneling Diagonally under an Urban River Embankment

The construction of urban cross-river tunnels usually requires passing under river embankments, which inevitably disturbs the embankment substratum and causes ground deformation. Previous engineering cases have shown that embankment settlement is greater than ordinary surface settlement and that uneven settlement results in cracks of in the embankment, reducing the embankment stability. Based on a cross-river tunnel project in China, the construction risks caused by the additional stress on the embankment substratum, asymmetrical embankment load, and shield tunneling in saturated fine sand are analyzed during a large-diameter slurry shield tunneling below an urban river embankment diagonally. Additionally, relevant risk control measures, such as slurry pressure, jacking thrust setting, and driving velocity in the saturated fine sand stratum, are evaluated. The results show that during shield tunneling under a diagonal urban river embankment, the additional stress and asymmetrical load effects should be considered, and the shield slurry pressure and jacking thrust should be adjusted according to the distance between the cutter head and the embankment. Furthermore, based on settlement monitoring data, the driving velocity of the shield should be reasonably adjusted in a timely manner to avoid disturbing the fine sand stratum below the embankment

A numerical study on the tensile splitting of concrete with digital image processing

Numerical simulations are performed to investigate the mechanical behavior of concrete in uniaxial compression test and tensile splitting test. Especially, the digital image processing (DIP) techniques are utilized to differentiate the interface types on the fracture surface of the specimen that is already split, which involves transforming the color image of the fracture surface into a binary image through graying, binarization, and opening operation processing. The boundary data obtained from the binary image is further processed by mirrored comparison and contour simplification, and is finally imported into the numerical model to reconstruct the different interface regions on the splitting surface. Different material properties are assigned to the corresponding interface regions through intensive programming with Python, whereby the influence of heterogeneity on the splitting process is analyzed through the established numerical model. Through comparison with homogeneous model, it is found that the heterogeneous model is capable of reproducing a more genuine fracturing process, with respect to the fracture initiation locations and splitting sequence of different interfaces. The proposed modeling schemes are valuable for potential researches exploring the failure process of the materials such as concretes and rocks whose mechanical behavior is influenced by their inherent heterogeneity