Highly integrated workflows for exploring cardiovascular conditions: Exemplars of precision medicine in Alzheimer's disease and aortic dissection

For precision medicine to be implemented through the lens of in silico technology, it is imperative that biophysical research workflows offer insight into treatments that are specific to a particular illness and to a particular subject. The boundaries of precision medicine can be extended using multiscale, biophysics-centred workflows that consider the fundamental underpinnings of the constituents of cells and tissues and their dynamic environments. Utilising numerical techniques that can capture the broad spectrum of biological flows within complex, deformable and permeable organs and tissues is of paramount importance when considering the core prerequisites of any state-of-the-art precision medicine pipeline. In this work, a succinct breakdown of two precision medicine pipelines developed within two Virtual Physiological Human (VPH) projects are given. The first workflow is targeted on the trajectory of Alzheimer's Disease, and caters for novel hypothesis testing through a multicompartmental poroelastic model which is integrated with a high throughput imaging workflow and subject-specific blood flow variability model. The second workflow gives rise to the patient specific exploration of Aortic Dissections via a multi-scale and compliant model, harnessing imaging, computational fluid-dynamics (CFD) and dynamic boundary conditions. Results relating to the first workflow include some core outputs of the multiporoelastic modelling framework, and the representation of peri-arterial swelling and peri-venous drainage solution fields. The latter solution fields were statistically analysed for a cohort of thirty-five subjects (stratified with respect to disease status, gender and activity level). The second workflow allowed for a better understanding of complex aortic dissection cases utilising both a rigid-wall model informed by minimal and clinically common datasets as well as a moving-wall model informed by rich datasets.

Leptin may play a role in bone microstructural alterations in obese children

CONTEXT

Bone mass is low and fracture risk is higher in obese children. Hormonal changes in relation to skeletal microstructure and biomechanics have not been studied in obese children.

OBJECTIVE

The objective of the study was to ascertain the relationships of obesity-related changes in hormones with skeletal microstructure and biomechanics.

DESIGN

High resolution peripheral quantitative computed tomography (HR-pQCT) was used to compare three-dimensional cortical and trabecular microstructure and biomechanics at load-bearing and nonload bearing sites in obese and lean children. The relationship between leptin, adiponectin, testosterone, estrogen, osteocalcin and sclerostin and skeletal microstructure was also determined.

SETTING

The study was conducted at a tertiary pediatric endocrine unit in the United Kingdom.

PARTICIPANTS

Obese and lean children were matched by gender and pubertal stage.

RESULTS

Radial cortical porosity (mean difference -0.01 [95% CI: -0.02, -0.004], P = .003) and cortical pore diameter (mean difference -0.005 mm [95% CI: -0.009, -0.001], P = .011) were lower in obese children. Tibial trabecular thickness was lower (mean difference -0.009 mm [95% CI: -0.014, -0.004], P = .003), and trabecular number was higher (mean difference 0.23 mm(-1) [95% CI: 0.08, 0.38], P = .004) in obese children. At the radius, fat mass percentage negatively correlated with cortical porosity (r = -0.57, P < .001) and pore diameter (r = -0.38, P = .02) and negatively correlated with trabecular thickness (r = -0.62, P < .001) and trabecular von Mises stress (r = -0.39, P = .019) at the tibia. No difference was observed in the other biomechanical parameters of the radius and tibia. Leptin was higher in obese children (805.3 ± 440.6 pg/ml vs 98.1 ± 75.4 pg/ml, P < .001) and was inversely related to radial cortical porosity (r = 0.60, 95% CI: [-0.80, -0.30], P < .001), radial cortical pore diameter (r = 0.51, 95% CI [-0.75, -0.16], P = .002), tibial trabecular thickness (r = 0.55, 95% CI: [-0.78, -0.21], P = .001) and tibial trabecular von Mises stress (r = -0.39, 95% CI: -0.65, 0.04, P = .02).

CONCLUSION

Childhood obesity alters radial and tibial microstructure. Leptin may direct these changes. Despite this, the biomechanical properties of the radius and tibia do not adapt sufficiently in obese children to withstand the increased loading potential from a fall. This may explain the higher incidence of fracture in obese children.

High-speed nonlinear finite element analysis for surgical simulation using graphics processing units

The use of biomechanical modelling, especially in conjunction with finite element analysis, has become common in many areas of medical image analysis and surgical simulation. Clinical employment of such techniques is hindered by conflicting requirements for high fidelity in the modelling approach, and fast solution speeds. We report the development of techniques for high-speed nonlinear finite element analysis for surgical simulation. We use a fully nonlinear total Lagrangian explicit finite element formulation which offers significant computational advantages for soft tissue simulation. However, the key contribution of the work is the presentation of a fast graphics processing unit (GPU) solution scheme for the finite element equations. To the best of our knowledge, this represents the first GPU implementation of a nonlinear finite element solver. We show that the present explicit finite element scheme is well suited to solution via highly parallel graphics hardware, and that even a midrange GPU allows significant solution speed gains (up to 16.8 x) compared with equivalent CPU implementations. For the models tested the scheme allows real-time solution of models with up to 16,000 tetrahedral elements. The use of GPUs for such purposes offers a cost-effective high-performance alternative to expensive multi-CPU machines, and may have important applications in medical image analysis and surgical simulation.

Characterization of the spliced leader genes and transcripts in Trypanosoma cruzi

Trypanosome mRNA is processed to maturity in a novel trans-splicing reaction during which a 35-nucleotide (nt) spliced leader (SL) is joined to the 5' ends of most structural gene transcripts. We have examined this process in Trypanosoma cruzi, the causative agent of Chagas' disease in Central and South America. In this communication, we characterize the genes encoding the SL (SL gene) in five different strains of T. cruzi by hybridization analysis and show that the genome of each of these strains contains numerous tandemly repeated copies of the SL gene. We demonstrate that the SL genes show remarkable intrastrain homogeneity, but significant interstrain heterogeneity. We have cloned and sequenced one of the SL repeats from T. cruzi strain CL and used synthetic oligodeoxyribonucleotides designed to hybridize to SL gene transcripts in Northern analyses of T. cruzi RNA to identify an approx. 110-nt putative SL primary transcript (SL-RNA). The 5' end of the SL-RNA was mapped to the first nt of the SL by primer extension analyses. The sequence of the 110-nt SL-RNA was used to generate a predicted secondary structure, and this structure compared favorably to the predicted secondary structures of SL transcripts of other trypanosomatids.