Two-dimensional intraventricular flow pattern visualization using the image-based computational fluid dynamics

The image-based computational fluid dynamics (IB-CFD) technique, as the combination of medical images and the CFD method, is utilized in this research to analyze the left ventricle (LV) hemodynamics. The research primarily aims to propose a semi-automated technique utilizing some freely available and commercial software packages in order to simulate the LV hemodynamics using the IB-CFD technique. In this research, moreover, two different physiological time-resolved 2D models of a patient-specific LV with two different types of aortic and mitral valves, including the orifice-type valves and integrated with rigid leaflets, are adopted to visualize the process of developing intraventricular vortex formation and propagation. The blood flow pattern over the whole cardiac cycle of two models is also compared to investigate the effect of utilizing different valve types in the process of the intraventricular vortex formation. Numerical findings indicate that the model with integrated valves can predict more complex intraventricular flow that can match better the physiological flow pattern in comparison to the orifice-type model.     

Computational biomechanics of human brain with and without the inclusion of the body under different blast orientation

Three different human head models in a free space are exposed to blast waves coming from four different directions. The four head–neck–body models composed of model a, with the neck free in space; model b, with neck fixed at the bottom; and model c, with the neck attached to the body. The results show that the effect of the body can be ignored for the first milliseconds of the head–blast wave interactions. Also one can see that although most biomechanical responses of the brain have similar patterns in all models, the shear stresses are heavily increased after a few milliseconds in model b in which the head motion is obstructed by the fixed-neck boundary conditions. The free-floating head model results are closer to the attached-body model.     

Fluid-solid interaction in arteries incorporating the autoregulation concept in boundary conditions

In pre-surgery decisions in hospital emergency cases, fast and reliable results of the solid and fluid mechanics problems are of great interest to clinicians. In the current investigation, an iterative process based on a pressure-type boundary condition is proposed in order to reduce the computational costs of blood flow simulations in arteries, without losing control of the important clinical parameters. The incorporation of cardiovascular autoregulation, together with the well-known impedance boundary condition, forms the basis of the proposed methodology. With autoregulation, the instabilities associated with conventional pressure-type or impedance boundary conditions are avoided without an excessive increase in computational costs. The general behaviour of pulsatile blood flow in arteries, which is important from the clinical point of view, is well reproduced through this new methodology. In addition, the interaction between the blood and the arterial walls occurs via a modified weak coupling, which makes the simulation more stable and computationally efficient. Based on in vitro experiments, the hyperelastic behaviour of the wall is characterised and modelled. The applications and benefits of the proposed pressure-type boundary condition are shown in a model of an idealised aortic arch with and without an ascending aorta dissection, which is a common cardiovascular disorder.     

Mechanobiology of low-density lipoprotein transport within an arterial wall—Impact of hyperthermia and coupling effects

The effects of hyperthermia, coupling attributes and property variations on Low-density lipoprotein (LDL) transport within a multi-layered wall while accounting for the fluid structure interaction (FSI) is analyzed in this work. To understand the potential impact of the hyperthermia process, thermo-induced attributes are incorporated, accounting for the plasma flow, mass transfer, as well as the elastic wall structure. The coupling effect of osmotic pressure, Soret and Dufour diffusion is discussed and their influence on LDL transport is examined, demonstrating that only the Soret effect needs to be accounted for. The effect of thermal expansion on changing the behavior of flow, mass transport, and elastic structure is illustrated and analyzed while incorporating the variations in the effective LDL diffusivity and consumption rate, as well as other dominating parameters. It is shown that hyperthermia results in an enhancement in LDL transport by increasing the concentration levels within the arterial wall.     

Plaque hemorrhage in carotid artery disease: Pathogenesis,clinical and biomechanical considerations

Stroke remains the most prevalent disabling illness today, with internal carotid artery luminal stenosis due to atheroma formation responsible for the majority of ischemic cerebrovascular events. Severity of luminal stenosis continues to dictate both patient risk stratification and the likelihood of surgical intervention. But there is growing evidence to suggest that plaque morphology may help improve pre-existing risk stratification criteria. Plaque components such a fibrous tissue, lipid rich necrotic core and calcium have been well investigated but plaque hemorrhage (PH) has been somewhat overlooked. In this review we discuss the pathogenesis of PH, its role in dictating plaque vulnerability, PH imaging techniques, marterial properties of atherosclerotic tissues, in particular, those obtained based on in vivo measurements and effect of PH in modulating local biomechanics.     

Simulation of Low Density Lipoprotein (LDL) permeation into multilayer coronary arterial wall: Interactive effects of wall shear stress and fluid-structure interaction in hypertension

Due to increased atherosclerosis-caused mortality, identification of its genesis and development is of great importance. Although, key factors of the origin of the disease is still unknown, it is widely believed that cholesterol particle penetration and accumulation in arterial wall is mainly responsible for further wall thickening and decreased rate of blood flow during a gradual progression. To date, various effective components are recognized whose simultaneous consideration would lead to a more accurate approximation of Low Density Lipoprotein (LDL) distribution within the wall. In this research, a multilayer Fluid-Structure Interaction (FSI) model is studied to simulate the penetration of LDL into the arterial wall. Distention impact on wall properties is taken into account by considering FSI and Wall Shear Stress (WSS) dependent endothelium properties. The results show intensified permeation of LDL whilst the FSI approach is applied. In addition, luminal distension prompted by FSI reduces WSS along lumen/wall interface, especially in hypertension. This effect leads to a lowered endothelial resistance against LDL permeation, comparing to the case in which WSS effect is overlooked. The results are in an acceptable consistency with the clinical researches on WSS effect on atherosclerosis development.     

Specific RNA-Binding Antibodies with a Four-Amino-Acid Code

Numerous large non-coding RNAs are rapidly being discovered, and many of them have been shown to play vital roles in gene expression, gene regulation, and human diseases. Given their often structured nature, specific recognition with an antibody fragment becomes feasible and may help define the structure and function of these non-coding RNAs. As demonstrated for protein antigens, specific antibodies may aid in RNA crystal structure elucidation or the development of diagnostic tools and therapeutic drugs targeting disease-causing RNAs. Recent success and limitation of RNA antibody development has made it imperative to generate an effective antibody library specifically targeting RNA molecules. Adopting the reduced chemical diversity design and further restricting the interface diversity to tyrosines, serines, glycines, and arginines only, we have constructed a RNA-targeting Fab library. Phage display selection and downstream characterization showed that this library yielded high-affinity Fabs for all three RNA targets tested. Using a quantitative specificity assay, we found that these Fabs are highly specific, possibly due to the alternate codon design we used to avoid consecutive arginines in the Fab interface. In addition, the effectiveness of the minimal Fab library may challenge our view of the protein–RNA binding interface and provide a unique solution for future design of RNA-binding proteins.     

Plasticity of the gene functions for DNA replication in the T4-like phages

We have completely sequenced and annotated the genomes of several relatives of the bacteriophage T4, including three coliphages (RB43, RB49 and RB69), three Aeromonas salmonicida phages (44RR2.8t, 25 and 31) and one Aeromonas hydrophila phage (Aeh1). In addition, we have partially sequenced and annotated the T4-like genomes of coliphage RB16 (a close relative of RB43), A. salmonicida phage 65, Acinetobacter johnsonii phage 133 and Vibrio natriegens phage nt-1. Each of these phage genomes exhibited a unique sequence that distinguished it from its relatives, although there were examples of genomes that are very similar to each other. As a group the phages compared here diverge from one another by several criteria, including (a) host range, (b) genome size in the range between approximately 160 kb and approximately 250 kb, (c) content and genetic organization of their T4-like genes for DNA metabolism, (d) mutational drift of the predicted T4-like gene products and their regulatory sites and (e) content of open-reading frames that have no counterparts in T4 or other known organisms (novel ORFs). We have observed a number of DNA rearrangements of the T4 genome type, some exhibiting proximity to putative homing endonuclease genes. Also, we cite and discuss examples of sequence divergence in the predicted sites for protein-protein and protein-nucleic acid interactions of homologues of the T4 DNA replication proteins, with emphasis on the diversity in sequence, molecular form and regulation of the phage-encoded DNA polymerase, gp43. Five of the sequenced phage genomes are predicted to encode split forms of this polymerase. Our studies suggest that the modular construction and plasticity of the T4 genome type and several of its replication proteins may offer resilience to mutation, including DNA rearrangements, and facilitate the adaptation of T4-like phages to different bacterial hosts in nature.     

A new formula for predicting the position of severe arterial stenosis

Noninvasive location of an occlusion or a severe stenosis in the arterial system is of a great interest for surgical interventions. Here, we present a new method to determine the location of arterial 99% stenosis in the arterial (sub) system. The method requires a measurement of propagation constant and the instantaneous flow rate or velocity at two sites of an arterial tree. The method was successfully tested using Womersley’s oscillatory flow theory and the data obtained by a simulation of Fluid structure interaction (FSI). The effect of noise has been investigated to simulate experimental conditions. The results demonstrate that location of 99% severe stenosis could be accurately obtained. The spatial resolution was approximately a few centimeters and the differences between exact and computed values didn’t exceed 13%. However, the identifications of stenotic sites decreased with the distance. Further investigation of the developed method in vivo and in vitro is required.