Comparison of LES of steady transitional flow in an idealized stenosed axisymmetric artery model with a RANS transitional model

In this study, two different turbulence methodologies are investigated to predict transitional flow in a 75% stenosed axisymmetric experimental arterial model and in a slightly modified version of the model with an eccentric stenosis. Large eddy simulation (LES) and Reynolds-averaged Navier-Stokes (RANS) methods were applied; in the LES simulations eddy viscosity subgrid-scale models were employed (basic and dynamic Smagorinsky) while the RANS method involved the correlation-based transitional version of the hybrid k-ε/k-ω flow model. The RANS simulations used 410,000 and 820,000 element meshes for the axisymmetric and eccentric stenoses, respectively, with y(+) less than 2 viscous wall units for the boundary elements, while the LES used 1,200,000 elements with y(+) less than 1. Implicit filtering was used for LES, giving an overlap between the resolved and modeled eddies, ensuring accurate treatment of near wall turbulence structures. Flow analysis was carried out in terms of vorticity and eddy viscosity magnitudes, velocity, and turbulence intensity profiles and the results were compared both with established experimental data and with available direct numerical simulations (DNSs) from the literature. The simulation results demonstrated that the dynamic Smagorinsky LES and RANS transitional model predicted fairly comparable velocity and turbulence intensity profiles with the experimental data, although the dynamic Smagorinsky model gave the best overall agreement. The present study demonstrated the power of LES methods, although they were computationally more costly, and added further evidence of the promise of the RANS transition model used here, previously tested in pulsatile flow on a similar model. Both dynamic Smagorinsky LES and the RANS model captured the complex transition phenomena under physiological Reynolds numbers in steady flow, including separation and reattachment. In this respect, LES with dynamic Smagorinsky appeared more successful than DNS in replicating the axisymmetric experimental results, although inflow conditions, which are subject to caveats, may have differed. For the eccentric stenosis, LES with Smagorinsky coefficient of 0.13 gave the closest agreement with DNS despite the known shortcomings of fixed coefficients. The relaminarization as the flow escaped the influence of the stenosis was amply demonstrated in the simulations, graphically so in the case of LES.     

Assimilation of water and dietary ions by the gastrointestinal tract during digestion in seawater-acclimated rainbow trout

Recent studies focusing on the consequences of feeding for ion and water balance in freshwater fish have revealed the need for similar comparative studies in seawater fish. A detailed time course sampling of gastrointestinal (GI) tract contents following the ingestion of a single meal of a commercial diet revealed the assimilation of both water and dietary ions (Na⁺, Cl^?, K⁺, Ca²⁺, Mg²⁺) along the GI tract of seawater-acclimated rainbow trout (Oncorhynchus mykiss) which had been fasted for 1 week. Consumption of the meal did not change the drinking rate. There was a large secretion of fluid into the anterior intestine and caecae (presumably bile and/or pancreatic secretions). As a result, net assimilation (63%) of the ingested water along the GI tract was lower than generally reported for fasted trout. Mg²⁺ was neither secreted into nor absorbed from the GI tract on a net basis. Only K⁺ (93% assimilated) and Ca²⁺ (43% assimilated) were absorbed in amounts in excess of those provided by ingested seawater, suggesting that dietary sources of K⁺ and Ca²⁺ may be important to seawater teleosts. The oesophagus–stomach served as a major site of absorption for Na⁺, Cl^?, K⁺, Ca²⁺, and Mg²⁺, and the anterior intestine and caecae as a major site of net secretion for all of these ions, except Cl^?. Despite large absorptive fluxes of these ions, the ionic composition of the plasma was maintained during the digestion of the meal. The results of the present study were compared with previous work on freshwater-acclimated rainbow trout, highlighting some important differences, but also several similarities on the assimilation of water and ions along the gastrointestinal tract during digestion. This study highlights the complicated array of ion and water transport that occurs in the intestine during digestion while revealing the importance of dietary K⁺ and Ca²⁺ to seawater-acclimated rainbow trout. Additionally, this study reveals that digestion in seawater-acclimated rainbow trout appears to compromise intestinal water absorption.     

Ultrahigh resolution and full-length pilin structures with insights for filament assembly, pathogenic functions, and vaccine potential

Pilin proteins assemble into Type IV pili (T4P), surface-displayed bacterial filaments with virulence functions including motility, attachment, transformation, immune escape, and colony formation. However, challenges in crystallizing full-length fiber-forming and membrane protein pilins leave unanswered questions regarding pilin structures, assembly, functions, and vaccine potential. Here we report pilin structures of full-length DnFimA from the sheep pathogen Dichelobacter nodosus and FtPilE from the human pathogen Francisella tularensis at 2.3 and 1 ? resolution, respectively. The DnFimA structure reveals an extended kinked N-terminal α-helix, an unusual centrally located disulfide, conserved subdomains, and assembled epitopes informing serogroup vaccines. An interaction between the conserved Glu-5 carboxyl oxygen and the N-terminal amine of an adjacent subunit in the crystallographic dimer is consistent with the hypothesis of a salt bridge between these groups driving T4P assembly. The FtPilE structure identifies an authentic Type IV pilin and provides a framework for understanding the role of T4P in F. tularensis virulence. Combined results define a unified pilin architecture, specialized subdomain roles in pilus assembly and function, and potential therapeutic targets.     

The effects of modeling simplifications on craniofacial finite element models: the alveoli (tooth sockets) and periodontal ligaments

Several finite element models of a primate cranium were used to investigate the biomechanical effects of the tooth sockets and the material behavior of the periodontal ligament (PDL) on stress and strain patterns associated with feeding. For examining the effect of tooth sockets, the unloaded sockets were modeled as devoid of teeth and PDL, filled with teeth and PDLs, or simply filled with cortical bone. The third premolar on the left side of the cranium was loaded and the PDL was treated as an isotropic, linear elastic material using published values for Young's modulus and Poisson's ratio. The remaining models, along with one of the socket models, were used to determine the effect of the PDL's material behavior on stress and strain distributions under static premolar biting and dynamic tooth loading conditions. Two models (one static and the other dynamic) treated the PDL as cortical bone. The other two models treated it as a ligament with isotropic, linear elastic material properties. Two models treated the PDL as a ligament with hyperelastic properties, and the other two as a ligament with viscoelastic properties. Both behaviors were defined using published stress-strain data obtained from in vitro experiments on porcine ligament specimens. Von Mises stress and strain contour plots indicate that the effects of the sockets and PDL material behavior are local. Results from this study suggest that modeling the sockets and the PDL in finite element analyses of skulls is project dependent and can be ignored if values of stress and strain within the alveolar region are not required.     

EBI2 operates independently of but in cooperation with CXCR5 and CCR7 to direct B cell migration and organization in follicles and the germinal center

Migration of B cells within lymphoid follicles is controlled by the chemokine receptors CXCR5 and CCR7 and the G-protein-coupled receptor EBI2 (GPR183). Whereas CXCR5 and CCR7 are known to mediate migration toward their respective chemokine ligands, it is unclear whether EBI2 acts by modulating these processes or by directly mediating chemotaxis toward its own spatially restricted ligand. It is also unknown how signals from these three receptors are integrated to control B cell localization. To answer these questions, we generated compound knockout mice deficient in expression of EBI2, CXCR5, or CCR7. Analysis of these mice revealed that EBI2 mediates B cell migration toward the outer areas of follicles and to bridging channels of the spleen independent of both CXCR5 and CCR7. Migratory signals delivered by EBI2 were shown to control B cell organization within the spleen and to be particularly important for positioning activated B cells in the early stages of Ab responses. An additional minor role for EBI2 was identified in the organization and affinity maturation of B cells in germinal centers. Thus, EBI2-mediated chemotaxis provides a third dimension to B cell migration that balances and integrates with the inputs from CXCR5 and CCR7 to determine B cell positioning.     

A PCSK9-binding antibody that structurally mimics the EGF(A) domain of LDL-receptor reduces LDL cholesterol in vivo

Proprotein convertase subtilisin-like/kexin type 9 (PCSK9) regulates LDL cholesterol levels by inhibiting LDL receptor (LDLr)-mediated cellular LDL uptake. We have identified a fragment antigen-binding (Fab) 1D05 which binds PCSK9 with nanomolar affinity. The fully human antibody 1D05-IgG2 completely blocks the inhibitory effects of wild-type PCSK9 and two gain-of-function human PCSK9 mutants, S127R and D374Y. The crystal structure of 1D05-Fab bound to PCSK9 reveals that 1D05-Fab binds to an epitope on the PCSK9 catalytic domain which includes the entire LDLr EGF(A) binding site. Notably, the 1D05-Fab CDR-H3 and CDR-H2 loops structurally mimic the EGF(A) domain of LDLr. In a transgenic mouse model (CETP/LDLr-hemi), in which plasma lipid and PCSK9 profiles are comparable to those of humans, 1D05-IgG2 reduces plasma LDL cholesterol to 40% and raises hepatic LDLr protein levels approximately fivefold. Similarly, in healthy rhesus monkeys, 1D05-IgG2 effectively reduced LDL cholesterol 20%-50% for over 2 weeks, despite its relatively short terminal half-life (t(1/2) = 3.2 days). Importantly, the decrease in circulating LDL cholesterol corresponds closely to the reduction in free PCSK9 levels. Together these results clearly demonstrate that the LDL-lowering effect of the neutralizing anti-PCSK9 1D05-IgG2 antibody is mediated by reducing the amount of PCSK9 that can bind to the LDLr.     

Picomolar nitric oxide signals from central neurons recorded using ultrasensitive detector cells

Nitric oxide (NO) is a widespread signaling molecule with potentially multifarious actions of relevance to health and disease. A fundamental determinant of how it acts is its concentration, but there remains a lack of coherent information on the patterns of NO release from its sources, such as neurons or endothelial cells, in either normal or pathological conditions. We have used detector cells having the highest recorded NO sensitivity to monitor NO release from brain tissue quantitatively and in real time. Stimulation of NMDA receptors, which are coupled to activation of neuronal NO synthase, routinely generated NO signals from neurons in cerebellar slices. The average computed peak NO concentrations varied across the anatomical layers of the cerebellum, from 12 to 130 pm. The mean value found in the hippocampus was 200 pm. Much variation in the amplitudes recorded by individual detector cells was observed, this being attributable to their location at variable distances from the NO sources. From fits to the data, the NO concentrations at the source surfaces were 120 pm to 1.4 nm, and the underlying rates of NO generation were 36-350 nm/s, depending on area. Our measurements are 4-5 orders of magnitude lower than reported by some electrode recordings in cerebellum or hippocampus. In return, they establish coherence between the NO concentrations able to elicit physiological responses in target cells through guanylyl cyclase-linked NO receptors, the concentrations that neuronal NO synthase is predicted to generate locally, and the concentrations that neurons actually produce.