•An enhanced particle shifting technique (PST) is presented to overcome the deficiencies of traditional PSTs.•The volume-non-conservation issue is tackled by introducing a corrective cohesion force ...between particles.•The non-physical gap issue is alleviated by introducing a different free-surface treatment.•Four benchmarks are implemented to validate the effectiveness and stability of the present scheme.•Satisfactory numerical results are obtained in WCSPH simulations of violent free-surface flows.
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The non-conservation of total fluid volume, caused by the accumulating errors on the potential energy of the fluid, has been a serious numerical issue in a Weakly-Compressible SPH (WCSPH) simulation when transitional Particle Shifting Techniques (PSTs) are employed to prevent disordered particle distribution and the tensile instability from negative pressures. This paper is dedicated to, within the framework of WCSPH, developing an enhanced version that remedies the aforementioned deficiency of the traditional PSTs, and meanwhile improves the quality of the particle distribution in the vicinity of a free-surface region. To this end, a Corrective Cohesion Force (CCF) between a target particle and its interacting particles is introduced to provide adaptive compensation corresponding to the particle repositioning. Four classical benchmarks are implemented to validate the effectiveness and stability of the present PST. It is demonstrated that the new PST incorporating with the CCF shows satisfactory performance to improve the conservation of total fluid volume, and to obtain more uniform particle distribution in the proximity of the free-surface. In addition, the newly-developed PST also maintains the accuracy and stability inherited from the traditional versions, suggesting that it can be treated as an ideal alternative with regard to the traditional PSTs in a WCSPH simulation, especially for a long-term-duration case with violent free-surface evolutions.
The recently developed FSI-SPH model (Sun et al., 2019c), by combining the multi-resolution δ+-SPH scheme and a Total Lagrangian SPH method, is further extended for more complex three-dimensional ...(3D) Fluid Structure Interaction (FSI) problems. The FSI-SPH model is strengthened with advanced numerical techniques, in which a combination of the Particle Shifting Technique (PST) and the Tensile Instability Control (TIC) is adopted to prevent flow voids induced by the tensile instability. The Adaptive Particle Refinement (APR) is used to refine particles in the boundary layer region and coarsen particles in the far-field to increase local accuracy but reduce overall computational cost. Moreover, the δ+-SPH and Total Lagrangian SPH solvers are coupled through a Modified Sequential Staggered (MSS) algorithm which, on one hand, ensures the numerical accuracy and stability and, on the other hand, improves the efficiency when magnitudes of time steps between the two solvers differ from each other significantly. In the numerical results, challenging 2D and 3D FSI cases are simulated to test the accuracy of the proposed FSI-SPH model. A new FSI benchmark with free-surface is proposed to highlight the advantage of this FSI-SPH model in simulating free-surface viscous flows. In addition, 3D effects in the FSI dam-breaking and sloshing cases are investigated.
•Multi-resolution δ+-SPH model is accurately and efficiently coupled with the Total Lagrangian SPH model.•Complex three-dimensional (3D) Fluid Structure Interaction (FSI) problems are simulated and validated.•A new benchmark named FSI4 is proposed.•The 3D effects in the FSI dam-breaking and sloshing cases are highlighted.
This article is dedicated to providing a detailed review concerning the SPH-based hydrodynamic simulations for ocean energy devices (OEDs). Attention is particularly focused on three topics that are ...tightly related to the concerning field, covering (1) SPH-based numerical fluid tanks, (2) multi-physics SPH techniques towards simulating OEDs, and finally (3) computational efficiency and capacity. In addition, the striking challenges of the SPH method with respect to simulating OEDs are elaborated, and the future prospects of the SPH method for the concerning topics are also provided.
CRISPR-Cas systems adapt “memories”
via
spacers from viruses and plasmids to develop adaptive immunity against mobile genetic elements. Mature CRISPR RNAs guide CRISPR-associated nucleases to ...site-specifically cleave target DNA or RNA, providing an efficient genome engineering tool for organisms of all three kingdoms. Cas9, Cas12, and Cas13 are single proteins with multiple domains that are the most widely used CRISPR nucleases of the Class 2 system. However, these CRISPR endonucleases are large in size, leading to difficulty for manipulation and toxicity for cells. Most archaeal genomes and half of the bacterial genomes encode different types of CRISPR-Cas systems. Therefore, developing endogenous CRISPR-Cas systems-based genome editing will simplify manipulations and increase editing efficiency in prokaryotic cells. Here, we review the current applications and discuss the prospects of using endogenous CRISPR nucleases for genome engineering and CRISPR-based antimicrobials.
This paper presents an improved particle shifting technology (IPST) for smoothed particle hydrodynamics (SPH). It allows particles in the vicinity of the free-surface to be shifted in all the ...directions in case they are not uniformly distributed, rather than just shifted tangentially to the free-surface in some conventional particle shifting technologies. Therefore, with the new technique, the imprecise shifting due to the inaccurate evaluations of the local normal and tangential vectors of the free-surface can be avoided, and a more uniform particle distribution near the free-surface can be obtained even for long-term simulations, which improves the accuracy and stability of the SPH method. Besides, by combining the advantages of two existing free-surface detection methods, an optimized detection approach is provided. It is capable of detecting the free-surface particles accurately, and meanwhile, it is easier to implement and requires lower computational costs, especially for three-dimensional problems. Several numerical tests show that the proposed IPST and the optimized free-surface detection method are robust and accurate for the simulation of a variety of free-surface flows.
•An improved particle shifting technology (IPST) in the SPH method is proposed.•An optimized free-surface detection method in SPH is introduced.•The accuracy and robustness of the proposed IPST is validated on several long-term simulations.
CDC14A codes for a conserved proline‐directed phosphatase, and mutations in the gene are associated with autosomal‐recessive severe to profound deafness, due to defective kinocilia. A role of CDC14A ...in cilia formation has also been described in other organisms. However, how human CDC14A impacts on cilia formation remains unclear. Here, we show that human RPE1 hCDC14APD cells, encoding a phosphatase dead version of hCDC14A, have longer cilia than wild‐type cells, while hCDC14A overexpression reduces cilia formation. Phospho‐proteome analysis of ciliated RPE1 cells identified actin‐associated and microtubule binding proteins regulating cilia length as hCDC14A substrates, including the actin‐binding protein drebrin. Indeed, we find that hCDC14A counteracts the CDK5‐dependent phosphorylation of drebrin at S142 during ciliogenesis. Further, we show that drebrin and hCDC14A regulate the recruitment of the actin organizer Arp2 to centrosomes. In addition, during ciliogenesis hCDC14A also regulates endocytosis and targeting of myosin Va vesicles to the basal body in a drebrin‐independent manner, indicating that it impacts primary cilia formation in a multilayered manner.
Synopsis
Human CDC14A negatively regulates primary cilia length in a multilayered manner by dephosphorylating actin‐associated proteins, including DBN1. Serine 142 of DBN1 is dephosphorylated by hCDC14A, thereby counteracting the cilia length promoting activity of CDK5.
hCDC14A localizes to the basal body and the actin cytoskeleton during ciliogenesis.
hCDC14A regulates the phosphorylation of DBN1, thereby contributing to cilia length control.
hCDC14A and DBN1 regulate the actin nucleator Arp2 at basal bodies.
Endocytosis and transport of myosin Va vesicles to the basal body is a DBN1‐independent function of hCDC14A during ciliogenesis.
Human CDC14A negatively regulates primary cilia length in a multilayered manner by dephosphorylating actin‐associated proteins, including DBN1. Serine 142 of DBN1 is dephosphorylated by hCDC14A, thereby counteracting the cilia length promoting activity of CDK5.
Conicity index, body-shape index, lipid accumulation product (LAP), waist circumference (WC), triglyceride, triglyceride-glucose (TyG) index, hepatic steatosis index (HSI), waist-to-height ratio ...(WHtR), TyG index-related parameters (TyG-WHtR, TyG-BMI, TyG-WC), body mass index (BMI), visceral adiposity index, triglyceride to high-density lipoprotein cholesterol ratio and body roundness index have been reported as reliable markers of non-alcoholic fatty liver disease (NAFLD). However, there is debate about which of the above obesity and lipid-related indices has the best predictive performance for NAFLD risk.
This study included 6870 female and 7411 male subjects, and 15 obesity and lipid-related indices were measured and calculated. NAFLD was diagnosed by abdominal ultrasound. The area under the curve (AUC) of 15 obesity and lipid-related indices were calculated by receiver operating characteristic (ROC) analysis.
Among the 15 obesity and lipid-related indices, the TyG index-related parameters had the strongest association with NAFLD. ROC analysis showed that except for ABSI, the other 14 parameters had high predictive value in identifying NAFLD, especially in female and young subjects. Most notably, TyG index-related parameters performed better than other parameters in predicting NAFLD in most populations. In the female population, the AUC of TyG-WC for predicting NAFLD was 0.9045, TyG-BMI was 0.9084, and TyG-WHtR was 0.9071. In the male population, the AUC of TyG-WC was 0.8356, TyG-BMI was 0.8428, and TyG-WHtR was 0.8372. In addition, BMI showed good NAFLD prediction performance in most subgroups (AUC>0.8).
Our data suggest that TyG index-related parameters, LAP, HSI, BMI, and WC appear to be good predictors of NAFLD. Of these parameters, TyG index-related parameters showed the best predictive potential.
Complex multiphase flow problems in ocean engineering have long been challenging topics. Problems such as large deformations at interfaces, multi-media interfaces, and multiple physical processes are ...difficult to simulate. Mesh-based algorithms could have limitations in dealing with multiphase interface capture and large interface deformations. On the contrary, the Smoothed Particle Hydrodynamics (SPH) method, as a Lagrangian meshless particle method, has some merit and flexibility in capturing multiphase interfaces and dealing with large boundary deformations. In recent years, with the improvement of SPH theory and numerical models, the SPH method has made significant advances and breakthroughs in terms of theoretical completeness and computational stability, which starts to be widely used in ocean engineering problems, including multiphase flows under atmospheric pressure, high-pressure multiphase flows, phase-change multiphase flows, granular multiphase flows and so on. In this paper, we review the progress of SPH theory and models in multiphase flow simulations, discussing the problems and challenges faced by the method, prospecting to future research works, and aiming to provide a reference for subsequent research.
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