Assessment of hemodynamic conditions in the aorta following root replacement with composite valve-conduit graft

This paper presents the analysis of detailed hemodynamics in the aortas of four patients following replacement with a composite bio-prosthetic valve-conduit. Magnetic resonance image-based computational models were set up for each patient with boundary conditions comprising subject-specific three-dimensional inflow velocity profiles at the aortic root and central pressure waveform at the model outlet. Two normal subjects were also included for comparison. The purpose of the study was to investigate the effects of the valve-conduit on flow in the proximal and distal aorta. The results suggested that following the composite valve-conduit implantation, the vortical flow structure and hemodynamic parameters in the aorta were altered, with slightly reduced helical flow index, elevated wall shear stress and higher non-uniformity in wall shear compared to normal aortas. Inter-individual analysis revealed different hemodynamic conditions among the patients depending on the conduit configuration in the ascending aorta, which is a key factor in determining post-operative aortic flow. Introducing a natural curvature in the conduit to create a smooth transition between the conduit and native aorta may help prevent the occurrence of retrograde and recirculating flow in the aortic arch, which is particularly important when a large portion or the entire ascending aorta needs to be replaced

Quantum mechanics in an evolving Hilbert space

Many basis sets for electronic structure calculations evolve with varying external parameters, such as moving atoms in dynamic simulations, giving rise to extra derivative terms in the dynamical equations. Here we revisit these derivatives in the context of differential geometry, thereby obtaining a more transparent formalization, and a geometrical perspective for better understanding the resulting equations. The effect of the evolution of the basis set within the spanned Hilbert space separates explicitly from the effect of the turning of the space itself when moving in parameter space, as the tangent space turns when moving in a curved space. New insights are obtained using familiar concepts in that context such as the Riemann curvature. The differential geometry is not strictly that for curved spaces as in general relativity, a more adequate mathematical framework being provided by fiber bundles. The language used here, however, will be restricted to tensors and basic quantum mechanics. The local gauge implied by a smoothly varying basis set readily connects with Berry's formalism for geometric phases. Generalized expressions for the Berry connection and curvature are obtained for a parameter-dependent occupied Hilbert space spanned by nonorthogonal Wannier functions. The formalism is applicable to basis sets made of atomic-like orbitals and also more adaptative moving basis functions (such as in methods using Wannier functions as intermediate or support bases), but should also apply to other situations in which nonorthogonal functions or related projectors should arise. The formalism is applied to the time-dependent quantum evolution of electrons for moving atoms. The geometric insights provided here allow us to propose new finite-difference time integrators, and also better understand those already proposed

Analysis of turbulence effects in a patient-specific aorta with aortic valve stenosis

Blood flow in the aorta is often assumed laminar, however aortic valve pathologies may induce transition to turbulence and our understanding of turbulence effects is incomplete. The aim of the study was to provide a detailed analysis of turbulence effects in aortic valve stenosis (AVS). Methods: Large-eddy simulation (LES) of flow through a patient-specific aorta with AVS was conducted. Magnetic resonance imaging (MRI) was performed and used for geometric reconstruction and patient-specific boundary conditions. Computed velocity field was compared with 4D flow MRI to check qualitative and quantitative consistency. The effect of turbulence was evaluated in terms of fluctuating kinetic energy, turbulence-related wall shear stress (WSS) and energy loss. Results: Our analysis suggested that turbulence was induced by a combination of a high velocity jet impinging on the arterial wall and a dilated ascending aorta which provided sufficient space for turbulence to develop. Turbulent WSS contributed to 40% of the total WSS in the ascending aorta and 38% in the entire aorta. Viscous and turbulent irreversible energy losses accounted for 3.9 and 2.7% of the total stroke work, respectively. Conclusions: This study demonstrates the importance of turbulence in assessing aortic haemodynamics in a patient with AVS. Neglecting the turbulent contribution to WSS could potentially result in a significant underestimation of the total WSS. Further work is warranted to extend the analysis to more AVS cases and patients with other aortic valve diseases

Evaluation of computational methodologies for accurate prediction of wall shear stress and turbulence parameters in a patient-specific aorta

Background: Recent studies suggest that blood flow in main arteries is intrinsically disturbed, even under healthy conditions. Despite this, many computational fluid dynamics (CFD) analyses of aortic haemodynamics make the assumption of laminar flow, and best practices surrounding appropriate modelling choices are lacking. This study aims to address this gap by evaluating different modelling and post-processing approaches in simulations of a patient-specific aorta. Methods: Magnetic resonance imaging (MRI) and 4D flow MRI from a patient with aortic valve stenosis were used to reconstruct the aortic geometry and derive patient-specific inlet and outlet boundary conditions. Three different computational approaches were considered based on assumed laminar or assumed disturbed flow states including low-resolution laminar (LR-laminar), high-resolution laminar (HR-Laminar) and large-eddy simulation (LES). Each simulation was ran for 30 cardiac cycles and post-processing was conducted on either the final cardiac cycle, or using a phase-averaged approach which utilised all 30 simulated cycles. Model capabilities were evaluated in terms of mean and turbulence-based parameters. Results: All simulation types, regardless of post-processing approach could correctly predict velocity values and flow patterns throughout the aorta. Lower resolution simulations could not accurately predict gradient-derived parameters including wall shear stress and viscous energy loss (largest differences up to 44.6% and 130.3%, respectively), although phase-averaging these parameters improved predictions. The HR-Laminar simulation produced more comparable results to LES with largest differences in wall shear stress and viscous energy loss parameters up to 5.1% and 11.6%, respectively. Laminar-based parameters were better estimated than turbulence-based parameters. Conclusions: Our findings suggest that well-resolved laminar simulations can accurately predict many laminar-based parameters in disturbed flows, but there is no clear benefit to running a HR-Laminar simulation over an LES simulation based on their comparable computational cost. Additionally, post-processing ‘typical’ laminar simulation results with a phase-averaged approach is a simple and cost-effective way to improve accuracy of lower-resolution simulation results

Melanocytic naevi and melanoma in survivors of childhood cancer.

There is evidence from previous studies of small numbers of children who received cytotoxic therapy for cancer, that they may develop increased numbers of melanocytic naevi (moles), the strongest known risk factors for melanoma. Our aim was to investigate a large number of survivors of childhood cancer in order to test the hypothesis that they have more melanocytic naevi than matched controls. Total-body naevus counts were obtained from 263 oncology patients ascertained in paediatric oncology departments in Queensland, Australia, and from 263 hospital controls matched for age and sex. Additional information was gathered from children's parents about concurrent factors influencing naevus development such as type of complexion and history of sun exposure. Matched analyses, both crude and adjusted for possible confounding factors, revealed no significant difference in overall density of naevi among oncology patients and control subjects, according to diagnosis or to duration or type of chemotherapy. However significantly more oncology patients had atypical naevi (P < 0.05) and acral naevi (P < 0.0001) than controls. One patient developed a malignant melanoma 13 years after chemotherapy and radiotherapy for rhabdomyosarcoma. These findings support an association between treatment for childhood cancer and acral naevi and suggest that atypical naevi may also be associated with chemotherapy in childhood

Deep learning cardiac motion analysis for human survival prediction

Motion analysis is used in computer vision to understand the behaviour of moving objects in sequences of images. Optimising the interpretation of dynamic biological systems requires accurate and precise motion tracking as well as efficient representations of high-dimensional motion trajectories so that these can be used for prediction tasks. Here we use image sequences of the heart, acquired using cardiac magnetic resonance imaging, to create time-resolved three-dimensional segmentations using a fully convolutional network trained on anatomical shape priors. This dense motion model formed the input to a supervised denoising autoencoder (4Dsurvival), which is a hybrid network consisting of an autoencoder that learns a task-specific latent code representation trained on observed outcome data, yielding a latent representation optimised for survival prediction. To handle right-censored survival outcomes, our network used a Cox partial likelihood loss function. In a study of 302 patients the predictive accuracy (quantified by Harrell's C-index) was significantly higher (p < .0001) for our model C=0.73 (95$\%$ CI: 0.68 - 0.78) than the human benchmark of C=0.59 (95$\%$ CI: 0.53 - 0.65). This work demonstrates how a complex computer vision task using high-dimensional medical image data can efficiently predict human survival

Development of experimental techniques for parameterization of multi-scale lithium-ion battery models

Presented here, is an extensive 35 parameter experimental data set of a cylindrical 21700 commercial cell (LGM50), for an electrochemical pseudo-two-dimensional (P2D) model. The experimental methodologies for tear-down and subsequent chemical, physical, electrochemical kinetics and thermodynamic analysis, and their accuracy and validity are discussed. Chemical analysis of the LGM50 cell shows that it is comprised of a NMC 811 positive electrode and bi-component Graphite-SiOx negative electrode. The thermodynamic open circuit voltages (OCV) and lithium stoichiometry in the electrode are obtained using galvanostatic intermittent titration technique (GITT) in half cell and three-electrode full cell configurations. The activation energy and exchange current coefficient through electrochemical impedance spectroscopy (EIS) measurements. Apparent diffusion coefficients are estimated using the Sand equation on the voltage transient during the current pulse; an expansion factor was applied to the bi-component negative electrode data to reflect the average change in effective surface area during lithiation. The 35 parameters are applied within a P2D model to show the fit to experimental validation LGM50 cell discharge and relaxation voltage profiles at room temperature. The accuracy and validity of the processes and the techniques in the determination of these parameters are discussed, including opportunities for further modelling and data analysis improvements

DNA repair biomarkers XPF and phospho-MAPKAP kinase 2 correlate with clinical outcome in advanced head and neck cancer.

BackgroundInduction chemotherapy is a common therapeutic option for patients with locoregionally-advanced head and neck cancer (HNC), but it remains unclear which patients will benefit. In this study, we searched for biomarkers predicting the response of patients with locoregionally-advanced HNC to induction chemotherapy by evaluating the expression pattern of DNA repair proteins.MethodsExpression of a panel of DNA-repair proteins in formalin-fixed paraffin embedded specimens from a cohort of 37 HNC patients undergoing platinum-based induction chemotherapy prior to definitive chemoradiation were analyzed using quantitative immunohistochemistry.ResultsWe found that XPF (an ERCC1 binding partner) and phospho-MAPKAP Kinase 2 (pMK2) are novel biomarkers for HNSCC patients undergoing platinum-based induction chemotherapy. Low XPF expression in HNSCC patients is associated with better response to induction chemoradiotherapy, while high XPF expression correlates with a worse response (p = 0.02). Furthermore, low pMK2 expression was found to correlate significantly with overall survival after induction plus chemoradiation therapy (p = 0.01), suggesting that pMK2 may relate to chemoradiation therapy.ConclusionsWe identified XPF and pMK2 as novel DNA-repair biomarkers for locoregionally-advanced HNC patients undergoing platinum-based induction chemotherapy prior to definitive chemoradiation. Our study provides insights for the use of DNA repair biomarkers in personalized diagnostics strategies. Further validation in a larger cohort is indicated

Reconciling the theoretical and experimental electronic structure of NbO2

Metal-insulator transition materials such as NbO2 have generated much excitement in recent years for their potential applications in computing and sensing. NbO2 has generated considerable debate over the nature of the phase transition, and the values for the band gap/band widths in the insulating phase. We present a combined theoretical and experimental study of the band gap and electronic structure of the insulating phase of NbO2. We carry out ab-initio density functional theory plus U calculations, directly determining U and J parameters for both the Nb 4d and O 2p subspaces through the recently introduced minimum-tracking linear response method. We find a fundamental bulk band gap of 0.80 eV for the full DFT+U+J theory. We also perform calculations and measurements for a (100) oriented thin film. Scanning tunnelling spectroscopy measurements show that the surface band gap varies from 0.75 eV to 1.35 eV due to an excess of oxygen in and near the surface region of the film. Slab calculations indicate metallicity localised at the surface region caused by an energy level shift consistent with a reduction in Coulomb repulsion. We demonstrate that this effect in combination with the simple, low cost DFT+U+J method can account for the band widths and p-d gap observed in X-ray photoelectron spectroscopy experiments. Overall, our results indicate the possible presence of a 2D anisotropic metallic layer at the (100) surface of NbO2.Comment: 11 pages, 5 figures, plus 3 pages of Supporting Informatio