Consistent lattice Boltzmann methods for incompressible axisymmetric flows

In this work, consistent lattice Boltzmann (LB) methods for incompressible axisymmetric flows are developed based on two efficient axisymmetric LB models available in the literature. In accord with their respective original models, the proposed axisymmetric models evolve within the framework of the standard LB method and the source terms contain no gradient calculations. Moreover, the incompressibility conditions are realized with the Hermite expansion, thus the compressibility errors arising in the existing models are expected to be reduced by the proposed incompressible models. In addition, an extra relaxation parameter is added to the Bhatnagar-Gross-Krook collision operator to suppress the effect of the ghost variable and thus the numerical stability of the present models is significantly improved. Theoretical analyses, based on the Chapman-Enskog expansion and the equivalent moment system, are performed to derive the macroscopic equations from the LB models and the resulting truncation terms (i.e., the compressibility errors) are investigated. In addition, numerical validations are carried out based on four well-acknowledged benchmark tests and the accuracy and applicability of the proposed incompressible axisymmetric LB models are verified.NRF (Natl Research Foundation, S’pore)Published versio

Forcing scheme analysis for the axisymmetric lattice Boltzmann method under incompressible limit

Because the standard lattice Boltzmann (LB) method is proposed for Cartesian Navier-Stokes (NS) equations, additional source terms are necessary in the axisymmetric LB method for representing the axisymmetric effects. Therefore, the accuracy and applicability of the axisymmetric LB models depend on the forcing schemes adopted for discretization of the source terms. In this study, three forcing schemes, namely, the trapezium rule based scheme, the direct forcing scheme, and the semi-implicit centered scheme, are analyzed theoretically by investigating their derived macroscopic equations in the diffusive scale. Particularly, the finite difference interpretation of the standard LB method is extended to the LB equations with source terms, and then the accuracy of different forcing schemes is evaluated for the axisymmetric LB method. Theoretical analysis indicates that the discrete lattice effects arising from the direct forcing scheme are part of the truncation error terms and thus would not affect the overall accuracy of the standard LB method with general force term (i.e., only the source terms in the momentum equation are considered), but lead to incorrect macroscopic equations for the axisymmetric LB models. On the other hand, the trapezium rule based scheme and the semi-implicit centered scheme both have the advantage of avoiding the discrete lattice effects and recovering the correct macroscopic equations. Numerical tests applied for validating the theoretical analysis show that both the numerical stability and the accuracy of the axisymmetric LB simulations are affected by the direct forcing scheme, which indicate that forcing schemes free of the discrete lattice effects are necessary for the axisymmetric LB method.NRF (Natl Research Foundation, S’pore)MOE (Min. of Education, S’pore)Published versio

Preparation of Monoclonal Antibody for Brevetoxin 1 and Development of Ic-ELISA and Colloidal Gold Strip to Detect Brevetoxin 1

Brevetoxin-1 (BTX-1), a marine toxin mostly produced by the dinoflagellatae Karenia brevis, has caused the death of marine organisms and has had numerous toxicological effects on human health. Hence, it is very necessary to develop a rapid, economical, and reliable immunoassay method for BTX-1 detection. In this study, two kinds of complete antigen were synthesized using the succinic anhydride and isobutyl chloroformate two-step methods. Conjugate BTX-1-OVA was used as an antigen for mice immunization, and BTX-1-BSA for measuring the titer of the produced antibodies. A hybridoma cell line 6C6 stably secreting monoclonal antibody (mAb) against BTX-1 was obtained by fusing SP2/0 myeloma cells with the spleen cells from the immunized mouse. The hybridoma 6C6 was injected into the abdomen of BALB/c mice to obtain ascites, and the anti-BTX-1 mAb was harvested from ascites by precipitation with caprylic acid/ammonium sulfate (CA-AS). The anti-BTX-1 mAb was identified as an IgG1 subtype, and the cross-reactivity results showed that anti-BTX-1 mAb was highly specific to BTX-1 with the affinity of 1.06 × 108 L/mol. The indirect competitive ELISA results indicated that the linear range for BTX-1 detection was 14–263 ng/mL with IC50 of 60 ng/mL, and a detection limit of 14 ng/mL. The average recovery rate from the spiked samples was 88 ± 2% in intra-assay and 89 ± 2% in inter-assay. The limit of detection (LOD) using the colloidal gold strip was 200 ng/mL with high specificity. Therefore, the anti-BTX-1 mAb can be used to detect BTX-1 in shellfish and other related samples

Genomic and transcriptomic features between primary and paired metastatic fumarate hydratase–deficient renal cell carcinoma

Abstract Background Fumarate hydratase–deficient renal cell carcinoma (FH-RCC) is a rare highly aggressive subtype of kidney cancer for which the distinct genomic, transcriptomic, and evolutionary relationships between metastatic and primary lesions are still unclear. Methods In this study, whole-exome, RNA-seq, and DNA methylation sequencing were performed on primary-metastatic paired specimens from 19 FH-RCC cases, including 23 primary and 35 matched metastatic lesions. Phylogenetic and clonal evolutionary analyses were used to investigate the evolutionary characteristics of FH-RCC. Transcriptomic analyses, immunohistochemistry, and multiple immunofluorescence experiments were performed to identify the tumor microenvironmental features of metastatic lesions. Results Paired primary and metastatic lesions generally showed similar characteristics of tumor mutation burden, tumor neoantigen burden, microsatellite instability score, CNV burden, and genome instability index. Notably, we identified an FH-mutated founding MRCA (the most recent common ancestor) clone that dominated the early evolutionary trajectories in FH-RCC. Although both primary and metastatic lesions manifested high immunogenicity, metastatic lesions exhibited higher enrichment of T effector cells and immune-related chemokines, together with upregulation of PD-L1, TIGIT, and BTLA. In addition, we found that concurrent NF2 mutation may be associated with bone metastasis and upregulation of cell cycle signature in metastatic lesions. Furthermore, although in FH-RCC metastatic lesions in general shared similar CpG island methylator phenotype with primary lesions, we found metastatic lesions displaying hypomethylated chemokine and immune checkpoints related genomic loci. Conclusions Overall, our study demonstrated the genomic, epigenomic, and transcriptomic features of metastatic lesions in FH-RCC and revealed their early evolutionary trajectory. These results provided multi-omics evidence portraying the progression of FH-RCC