Optimizing the geometrical accuracy of curvilinear meshes

This paper presents a method to generate valid high order meshes with optimized geometrical accuracy. The high order meshing procedure starts with a linear mesh, that is subsequently curved without taking care of the validity of the high order elements. An optimization procedure is then used to both untangle invalid elements and optimize the geometrical accuracy of the mesh. Standard measures of the distance between curves are considered to evaluate the geometrical accuracy in planar two-dimensional meshes, but they prove computationally too costly for optimization purposes. A fast estimate of the geometrical accuracy, based on Taylor expansions of the curves, is introduced. An unconstrained optimization procedure based on this estimate is shown to yield significant improvements in the geometrical accuracy of high order meshes, as measured by the standard Haudorff distance between the geometrical model and the mesh. Several examples illustrate the beneficial impact of this method on CFD solutions, with a particular role of the enhanced mesh boundary smoothness.Comment: Submitted to JC

X-Mesh: A new approach for the simulation of two-phase flow with sharp interface

Accurate modeling of moving boundaries and interfaces is a difficulty present in many situations of computational mechanics. We use the eXtreme Mesh deformation approach (X-Mesh) to simulate the interaction between two immiscible flows using the finite element method, while maintaining an accurate and sharp description of the interface without remeshing. In this new approach, the mesh is locally deformed to conform to the interface at all times, which can result in degenerated elements. The surface tension between the two fluids is added by imposing the pressure jump condition at the interface, which, when combined with the X-Mesh framework, allows us to have an exactly sharp interface. If a numerical scheme fails to properly balance surface tension and pressure gradients, it leads to numerical artefacts called spurious or parasitic currents. The method presented here is well balanced and reduces such currents down to the level of machine precision

Behavioural and oceanographic isolation of an island‑based jellyfish (Copula sivickisi, Class Cubozoa) population

Cubozoan jellyfish are classified as plankton despite the strong swimming and orientation abilities of cubomedusae. How these capabilities could affect cubozoan population structures is poorly understood. Medusae of the cubozoan Copula sivickisi can uniquely attach to surfaces with the sticky pads on their bells. Biophysical modelling was used to investigate the spatial scales of connectivity in a C. sivickisi population. When the medusae were active at night they could maintain their observed distribution on fringing reef if they attached to the reef when the current speed exceeded a moderate threshold. This behaviour facilitated the isolation of a C. sivickisi population on reefs fringing Magnetic Island, Queensland, Australia. Within this distribution, there was considerable within bay retention and medusae rarely travelled > 3 km. The few (< 0.1%) medusae lost from the island habitat were largely advected into open water and away from the mainland coast which lies 8 km from the island. Given that successful emigration is unlikely, the island population probably represents a stock that is ecologically distinct from any mainland populations. The cosmopolitan distribution of C. sivickisi could contain incipient or cryptic species given the small scales of connectivity demonstrated here

The X-Mesh method applied to Multiphase Flows

The accurate modeling of moving boundaries and interfaces is a difficulty present in many situations in computational mechanics. In this paper we use a new approach, X-Mesh, to simulate with the finite element method the interaction between two immiscible fluids while keeping an accurate description of the interface without mesh regeneration. The method is validated with complex problems such as Rayleigh-Taylor instabilities, sloshing and dambreak. The quality of the results and the efficiency of the method show the potential of this approach to simulate such physical phenomena

Fine-Scale Coral Connectivity Pathways in the Florida Reef Tract: Implications for Conservation and Restoration

Connectivity between coral reefs is critical to ensure their resilience and persistence against disturbances. It is driven by ocean currents, which often have very complex patterns within reef systems. Only biophysical models that simulate both the fine-scale details of ocean currents and the life-history traits of larvae transported by these currents can help to estimate connectivity in large reef systems. Here we use the unstructured-mesh coastal ocean model SLIM that locally achieves a spatial resolution of ~100 m, 10 times finer than existing models, over the entire Florida Reef Tract (FRT). It allows us to simulate larval dispersal between the ~1,000 reefs composing the FRT. By using different connectivity measures and clustering methods, we have identified two major connectivity pathways, one originating on the westernmost end of the outer shelf and the other originating on the inner shelf, North of the Lower Keys. We introduce new connectivity indicators, based on the PageRank algorithm, to show that protection efforts should be focused on the most upstream reefs of each pathway, while reefs best suited for restoration are more evenly spread between the Lower and Upper Keys. We identify one particular reef, North of Vaca Key, that is a major stepping stone in the connectivity network. Our results are the first reef-scale connectivity estimates for the entire FRT. Such fine-scale information can provide knowledge-based decision support to allocate conservation and restoration resources optimally

ABCB1 (MDR1) polymorphisms and ovarian cancer progression and survival: A comprehensive analysis from the Ovarian Cancer Association Consortium and The Cancer Genome Atlas

&lt;b&gt;Objective&lt;/b&gt; &lt;i&gt;ABCB1&lt;/i&gt; encodes the multi-drug efflux pump P-glycoprotein (P-gp) and has been implicated in multi-drug resistance. We comprehensively evaluated this gene and flanking regions for an association with clinical outcome in epithelial ovarian cancer (EOC).&lt;p&gt;&lt;/p&gt; &lt;b&gt;Methods&lt;/b&gt; The best candidates from fine-mapping analysis of 21 &lt;i&gt;ABCB1&lt;/i&gt; SNPs tagging C1236T (rs1128503), G2677T/A (rs2032582), and C3435T (rs1045642) were analysed in 4616 European invasive EOC patients from thirteen Ovarian Cancer Association Consortium (OCAC) studies and The Cancer Genome Atlas (TCGA). Additionally we analysed 1,562 imputed SNPs around ABCB1 in patients receiving cytoreductive surgery and either ‘standard’ first-line paclitaxel–carboplatin chemotherapy (n = 1158) or any first-line chemotherapy regimen (n = 2867). We also evaluated ABCB1 expression in primary tumours from 143 EOC patients.&lt;p&gt;&lt;/p&gt; &lt;b&gt;Result&lt;/b&gt; Fine-mapping revealed that rs1128503, rs2032582, and rs1045642 were the best candidates in optimally debulked patients. However, we observed no significant association between any SNP and either progression-free survival or overall survival in analysis of data from 14 studies. There was a marginal association between rs1128503 and overall survival in patients with nil residual disease (HR 0.88, 95% CI 0.77–1.01; p = 0.07). In contrast, &lt;i&gt;ABCB1&lt;/i&gt; expression in the primary tumour may confer worse prognosis in patients with sub-optimally debulked tumours.&lt;p&gt;&lt;/p&gt; &lt;b&gt;Conclusion&lt;/b&gt; Our study represents the largest analysis of &lt;i&gt;ABCB1&lt;/i&gt; SNPs and EOC progression and survival to date, but has not identified additional signals, or validated reported associations with progression-free survival for rs1128503, rs2032582, and rs1045642. However, we cannot rule out the possibility of a subtle effect of rs1128503, or other SNPs linked to it, on overall survival.&lt;p&gt;&lt;/p&gt

Early Experience With Uniplanar Versus Biplanar Expandable Interbody Fusion Devices in Single-Level Minimally Invasive Transforaminal Lumbar Interbody Fusion

ObjectiveTo compare the early radiographic and clinical outcomes of expandable uniplanar versus biplanar interbody cages used for single-level minimally invasive transforaminal lumbar interbody fusion (MIS-TLIF). MethodA retrospective review of 1-level MIS-TLIFs performed with uniplanar and biplanar polyetheretherketone cages was performed. Radiographic measurements were performed on radiographs taken preoperatively, at 6-week follow-up, and 1-year follow-up. Oswestry Disability Index (ODI) and visual analogue scale (VAS) for back and leg at 3-month and 1-year follow-up. ResultsA total of 93 patients (41 uniplanar, 52 biplanar) were included. Both cage types provided significant postoperative improvements in anterior disc height, posterior disc height, and segmental lordosis at 1 year. No significant differences in cage subsidence rates were found between uniplanar (21.9%) and biplanar devices (32.7%) at 6 weeks (odds ratio, 2.015; 95% confidence interval, 0.651–6.235; p = 0.249) with no additional instances of subsidence at 1 year. No significant differences in the magnitude of improvements based on ODI, VAS back, or VAS leg at 3-month or 1-year follow-up between groups and the proportion of patients achieving the minimal clinically important difference in ODI, VAS back, or VAS leg at 1 year were not statistically significantly different (p \u3e 0.05). Finally, there were no significant differences in complication rates (p = 0.283), 90-day readmission rates (p = 1.00), revision surgical procedures (p = 0.423), or fusion rates at 1 year (p = 0.457) between groups. ConclusionsBiplanar and uniplanar expandable cages offer a safe and effective means of improving anterior disc height, posterior disc height, segmental lordosis, and patient-reported outcome measures at 1 year postoperatively. No significant differences in radiographic outcomes, subsidence rates, mean subsidence distance, 1-year patient-reported outcomes, and postoperative complications were noted between groups