Study of an infant brain subjected to periodic motion via a custom experimental apparatus design and finite element modelling

This paper presents a rig that was specifically designed to simulate the shaking of mechanical models of biological systems, especially those related to shaken baby syndrome (SBS). The scope of this paper includes the testing of an anthropomorphic model that simulates an infant head and provides validation data for complex finite element (FE) modelling using three numerical methods (Lagrangian, Arbitrary-Lagrangian–Eulerian (ALE) and Eulerian method) for fluid structure coupling.The experiments for this study aim to provide an understanding of the influence of two factors on intracranial brain movement of the infant head during violent shaking: (1) the specific paediatric head structure: the anterior fontanelle and (2) the brain–skull interface.The results show that the Eulerian analysis method has significant advantages for the FSI modelling of brain–CSF–skull interactions over the more commonly used methods, e.g. the Lagrangian method. To the knowledge of the authors, this methodology has not been discussed in previous publication.The results indicate that the biomechanical investigation of SBS can provide more accurate results only if the skull with paediatric features and the brain–skull interface are correctly represented, which were overlooked in previous SBS studies.     

Three-dimensional flows in a hyperelastic vessel under external pressure

We study the collapsible behaviour of a vessel conveying viscous flows subject to external pressure, a scenario that could occur in many physiological applications. The vessel is modelled as a three-dimensional cylindrical tube of nonlinear hyperelastic material. To solve the fully coupled fluid–structure interaction, we have developed a novel approach based on the Arbitrary Lagrangian–Eulerian (ALE) method and the frontal solver. The method of rotating spines is used to enable an automatic mesh adaptation. The numerical code is verified extensively with published results and those obtained using the commercial packages in simpler cases, e.g. ANSYS for the structure with the prescribed flow, and FLUENT for the fluid flow with prescribed structure deformation. We examine three different hyperelastic material models for the tube for the first time in this context and show that at the small strain, all three material models give similar results. However, for the large strain, results differ depending on the material model used. We further study the behaviour of the tube under a mode-3 buckling and reveal its complex flow patterns under various external pressures. To understand these flow patterns, we show how energy dissipation is associated with the boundary layers created at the narrowest collapsed section of the tube, and how the transverse flow forms a virtual sink to feed a strong axial jet. We found that the energy dissipation associated with the recirculation does not coincide with the flow separation zone itself, but overlaps with the streamlines that divide the three recirculation zones. Finally, we examine the bifurcation diagrams for both mode-3 and mode-2 collapses and reveal that multiple solutions exist for a range of the Reynolds number. Our work is a step towards modelling more realistic physiological flows in collapsible arteries and veins.     

Frictional contact mechanics methods for soft materials: application to tracking breast cancers

Mammography is currently the most widely used screening and diagnostic tool for breast cancer. Because X-ray images are 2D projections of a 3D object, it is not trivial to localise features identified in mammogram pairs within the breast volume. Furthermore, mammograms represent highly deformed configurations of the breast under compression, thus the tumour localisation process relies on the clinician's experience. Biomechanical models of the breast undergoing mammographic compressions have been developed to overcome this limitation. In this study, we present the development of a modelling framework that implements Coulomb's frictional law with a finite element analysis using a C(1)-continuous Hermite mesh. We compared two methods of this contact mechanics implementation: the penalty method, and the augmented Lagrangian method, the latter of which is more accurate but computationally more expensive compared to the former. Simulation results were compared with experimental data from a soft silicon gel phantom in order to evaluate the modelling accuracy of each method. Both methods resulted in surface-deformation root-mean-square errors of less than 2mm, whilst the maximum internal marker prediction error was less than 3mm when simulating two mammographic-like compressions. Simulation results were confirmed using the augmented Lagrangian method, which provided similar accuracy. We conclude that contact mechanics on soft elastic materials using the penalty method with an appropriate choice of the penalty parameters provides sufficient accuracy (with contact constraints suitably enforced), and may thus be useful for tracking breast tumours between clinical images.     

Finite element modelling approaches for well-ordered porous metallic materials for orthopaedic applications: cost effectiveness and geometrical considerations

The mechanical properties of well-ordered porous materials are related to their geometrical parameters at the mesoscale. Finite element (FE) analysis is a powerful tool to design well-ordered porous materials by analysing the mechanical behaviour. However, FE models are often computationally expensive. This article aims to develop a cost-effective FE model to simulate well-ordered porous metallic materials for orthopaedic applications. Solid and beam FE modelling approaches are compared, using finite size and infinite media models considering cubic unit cell geometry. The model is then applied to compare two unit cell geometries: cubic and diamond. Models having finite size provide similar results than the infinite media model approach for large sample sizes. In addition, these finite size models also capture the influence of the boundary conditions on the mechanical response for small sample sizes. The beam FE modelling approach showed little computational cost and similar results to the solid FE modelling approach. Diamond unit cell geometry appeared to be more suitable for orthopaedic applications than the cubic unit cell geometry.     

Validation and Application of Skeletochronology for Age Determination of the Ryukyu Ground Gecko,Goniurosaurus kuroiwae （Squamata： Eublepharidae）

Skeletochronology is a method commonly used for estimating the age of amphibians and reptiles in the wild. However, the number of lines of arrested growth （LAGs） does not necessarily reflect age in some species. We validated the applicability of this method to an endangered eublepharid gecko, Goniurosaurus kuroiwae, then inferred its longevity and age structures in wild populations. We classified young geckos into three groups using previously published data for early growth： Group 1 contained hatchlings before the first winter, Group 2 contained hatchlings after the first win- ter, and Group 3 included yearlings after the second winter. LAG numbers in these groups were then compared. All individuals in Group 1 possessed a single LAG, which was considered as a hatching line. Most individuals in Groups 2 and 3 possessed one and two additional LAGs, respectively （LAG1 and LAG2）, corroborating the notion that LAGs are formed annually. A few geckos exhibited fewer LAGs than expected. Analysis of variations in LAG and marrow cavity diameter demonstrated that in animals with fewer LAGs, endosteal resorption or fusion of hatching line and LAG1 had occurred. LAG2 was never lost by endosteal resorption and was identifiable by its diameter. Thus, the age of adult geckos could be determined by counting LAGs outward from LAG2. Application of this method to wild populations re- vealed that the longevity of this species is not less than 83 months, but that almost all individuals in fragmented habitats die before 50 months, suggesting lower population sustainability in such habitats.     

Towards autonomic performance management of large scale data centers using interaction balance principle

In this paper, an autonomic performance management approach is introduced that can be applied to a general class of web services deployed in large scale distributed environment. The proposed approach utilizes traditional large scale control-based algorithms by using interaction balance approach in web service environment for managing the response time and the system level power consumption. This approach is developed in a generic fashion that makes it suitable for web service deployments, where web service performance can be adjusted by using a finite set of control inputs. This approach maintains the service level agreements, maximizes the revenue, and minimizes the infrastructure operating cost. Additionally, the proposed approach is fault-tolerant with respect to the failures of the computing nodes inside the distributed deployment. Moreover, the computational overhead of the proposed approach can also be managed by using appropriate value of configuration parameters during its deployment.     

Mechanical hemolysis in blood flow: user-independent predictions with the solution of a partial differential equation

This paper presents for the first time numerical predictions of mechanical blood hemolysis obtained by solving a hyperbolic partial differential equation (PDE) modelling the hemolysis in a Eulerian frame of reference. This provides hemolysis predictions over the entire computational domain as an alternative to the Lagrangian approach consisting in evaluating cell hemolysis along their trajectories. The solution of a PDE over a computational domain, such as in the approach presented herein, yields a unique solution. This is a clear advantage over the Lagrangian approach, which requires the human-made choice of a limited number of trajectories for integration and inevitably results in the incomplete coverage of the computational domain. The hyperbolic hemolysis model is solved with a Discontinuous Galerkin finite element method. The solution algorithm also includes adaptive remeshing to provide high accuracy simulations. Predictions of the modified index of hemolysis (MIH) are presented for flows in dialysis cannulae and sudden contractions. MIH predictions for cannulae differ significantly from those obtained by other authors using the Lagrangian approach. The predictions for flows in sudden contractions are used, along with our own experimental measurements, to assess the value of the threshold shear stress required for hemolysis that is included in the hemolysis model.     

A New Asynchronous Parallel Algorithm for Inferring Large-Scale Gene Regulatory Networks

The reconstruction of gene regulatory networks (GRNs) from high-throughput experimental data has been considered one of the most important issues in systems biology research. With the development of high-throughput technology and the complexity of biological problems, we need to reconstruct GRNs that contain thousands of genes. However, when many existing algorithms are used to handle these large-scale problems, they will encounter two important issues: low accuracy and high computational cost. To overcome these difficulties, the main goal of this study is to design an effective parallel algorithm to infer large-scale GRNs based on high-performance parallel computing environments. In this study, we proposed a novel asynchronous parallel framework to improve the accuracy and lower the time complexity of large-scale GRN inference by combining splitting technology and ordinary differential equation (ODE)-based optimization. The presented algorithm uses the sparsity and modularity of GRNs to split whole large-scale GRNs into many small-scale modular subnetworks. Through the ODE-based optimization of all subnetworks in parallel and their asynchronous communications, we can easily obtain the parameters of the whole network. To test the performance of the proposed approach, we used well-known benchmark datasets from Dialogue for Reverse Engineering Assessments and Methods challenge (DREAM), experimentally determined GRN of Escherichia coli and one published dataset that contains more than 10 thousand genes to compare the proposed approach with several popular algorithms on the same high-performance computing environments in terms of both accuracy and time complexity. The numerical results demonstrate that our parallel algorithm exhibits obvious superiority in inferring large-scale GRNs.     

Plasmodium berghei and Eperythrozoon coccoides: Antibody and immunoglobulin synthesis in germfree and and conventional mice simultaneously infected

The immune response to Eperythrozoon coccoides and the malaria parasite Plasmodium berghei was evaluated in germfree (GF) and conventionally reared (CV) mice infected with both parasites. Following infection, the mice showed significant changes in the levels of the immunoglobulins IgM, 7Sγin1, 7Sγ2a, and 7Sγ2b, but no detectable changes in IgA. Increases in immunoglobulin levels were first observed in GF mice, but by the twelth day both GF and CV mice had comparable levels. 7Sγ2a globulin had a bimodal distribution in both groups of mice which probably was due to heterogeneity in the allotype of this immunoglobulin. IgM levels closely paralleled the antibody responses to P. berghei suggesting that most of the antibody to this parasite was IgM. Relatively low levels of antibody to both parasites, in comparison to the large immunoglobulin response, were detected in GF and CV mice. The possible causes for the low titers are discussed.     

A fault detection service for wide area distributed computations

The potential for faults in distributed computing systems is a significant complicating factor for application developers. While a variety of techniques exist for detecting and correcting faults, the implementation of these techniques in a particular context can be difficult. Hence, we propose a fault detection service designed to be incorporated, in a modular fashion, into distributed computing systems, tools, or applications. This service uses well-known techniques based on unreliable fault detectors to detect and report component failure, while allowing the user to trade off timeliness of reporting against false positive rates. We describe the architecture of this service, report on experimental results that quantify its cost and accuracy, and describe its use in two applications, monitoring the status of system components of the GUSTO computational grid testbed and as part of the NetSolve network-enabled numerical solver. This revised version was published online in July 2006 with corrections to the Cover Date.     

A case study on qualitative model evaluation using data about river water quality

Qualitative reasoning has been successfully used for ecological modelling, particularly when numerical data are not available. However, in order to further explore the potential of this modelling approach, it is important to discuss how to incorporate numerical data, if available, and to develop means to evaluate conceptual aspects and model outputs. This paper describes a study on qualitative model evaluation, in which numerical data about water quality are used to define different scenarios in a water basin, so that the outputs of simulations with the model can be compared to the actual system. The model was evaluated by independent experts, concerning its conceptual and operational aspects, and with respect to its predictive capability. The model was considered valid for the intended use, which is to increase the understanding of non-expert water managers.     

A Pressure-dependent Model for the Regulation of Lipoprotein Lipase by Apolipoprotein C-II

Apolipoprotein C-II (apoC-II) is the co-factor for lipoprotein lipase (LPL) at the surface of triacylglycerol-rich lipoproteins. LPL hydrolyzes triacylglycerol, which increases local surface pressure as surface area decreases and amphipathic products transiently accumulate at the lipoprotein surface. To understand how apoC-II adapts to these pressure changes, we characterized the behavior of apoC-II at multiple lipid/water interfaces. ApoC-II adsorption to a triacylglycerol/water interface resulted in large increases in surface pressure. ApoC-II was exchangeable at this interface and desorbed on interfacial compressions. These compressions increase surface pressure and mimic the action of LPL. Analysis of gradual compressions showed that apoC-II undergoes a two-step desorption, which indicates that lipid-bound apoC-II can exhibit at least two conformations. We characterized apoC-II at phospholipid/triacylglycerol/water interfaces, which more closely mimic lipoprotein surfaces. ApoC-II had a large exclusion pressure, similar to that of apoC-I and apoC-III. However, apoC-II desorbed at retention pressures higher than those seen with the other apoCs. This suggests that it is unlikely that apoC-I and apoC-III inhibit LPL via displacement of apoC-II from the lipoprotein surface. Upon rapid compressions and re-expansions, re-adsorption of apoC-II increased pressure by lower amounts than its initial adsorption. This indicates that apoC-II removed phospholipid from the interface upon desorption. These results suggest that apoC-II regulates the activity of LPL in a pressure-dependent manner. ApoC-II is provided as a component of triacylglycerol-rich lipoproteins and is the co-factor for LPL as pressure increases. Above its retention pressure, apoC-II desorbs and removes phospholipid. This triggers release of LPL from lipoproteins.     

Artichoke leave extract for chronic hepatitis C – A pilot study

BackgroundArtichoke leave extracts (ALE) have hepatoprotektive properties and are used by patients with chronic liver disease. Effects in patients with chronic hepatitis C are unclear.Methods17 patients with chronic hepatitis C and persistently elevated aminotransferase levels were treated for 12 weeks with 3200 mg standardized ALE per day. Primary outcome parameter was the rate of alanine aminotransferase (ALT) normalisation after 12 weeks. Secondary parameters were the course of ALT, aspartate aminotransferase and γ glutamyltransferase levels, quantitative HCV RNA, subjective symptoms frequently associated with chronic hepatitis C (fatigue, discomfort upper abdomen, joint problems) and safety.ResultsNone of the patients had normalized ALT levels after 12 weeks of treatment. There was no significant change of aminotransferase levels or viral load compared to baseline levels. Fatigue and joint problems significantly improved after 4 weeks of treatment. However, after 12 weeks, there was no significant difference to baseline. Tolerability of ALE was rated as good to excellent. Severe side effects did not occur.ConclusionALE seem not to be effective to improve aminotransferase levels in patients with chronic hepatitis C     

Green flexible opportunistic computing with task consolidation and virtualization

Energy efficiency and high computing power are basic design considerations across modern-day computing solutions due to different concerns such as system performance, operational cost, and environmental issues. Desktop Grid and Volunteer Computing System (DGVCS) so called opportunistic infrastructures offer computational power at low cost focused on harvesting idle computing cycles of existing commodity computing resources. Other than allowing to customize the end user offer, virtualization is considered as one key techniques to reduce energy consumption in large-scale systems and contributes to the scalability of the system. This paper presents an energy efficient approach for opportunistic infrastructures based on task consolidation and customization of virtual machines. The experimental results with single desktops and complete computer rooms show that virtualization significantly improves the energy efficiency of opportunistic grids compared with dedicated computing systems without disturbing the end-user.     

A robust and readily implementable method for the meta-analysis of response ratios with and without missing standard deviations

The log response ratio, lnRR, is the most frequently used effect size statistic for meta-analysis in ecology. However, often missing standard deviations (SDs) prevent estimation of the sampling variance of lnRR. We propose new methods to deal with missing SDs via a weighted average coefficient of variation (CV) estimated from studies in the dataset that do report SDs. Across a suite of simulated conditions, we find that using the average CV to estimate sampling variances for all observations, regardless of missingness, performs with minimal bias. Surprisingly, even with missing SDs, this simple method outperforms the conventional approach (basing each effect size on its individual study-specific CV) with complete data. This is because the conventional method ultimately yields less precise estimates of the sampling variances than using the pooled CV from multiple studies. Our approach is broadly applicable and can be implemented in all meta-analyses of lnRR, regardless of ‘missingness’.     

Geographical and interannual variability in biomass partitioning in grassland ecosystems: a synthesis of field data

Biomass partitioning is an important variable in terrestrial ecosystem carbon modeling. However, geographical and interannual variability in f(BNPP), defined as the fraction of belowground net primary productivity (BNPP) to total NPP, and its relationship with climatic variables, have not been explored. Here we addressed these issues by synthesizing 94 site-year field biomass data at 12 grassland sites around the world from a global NPP database and from the literature. Results showed that f(BNPP) varied from 0.40 to 0.86 across 12 sites. In general, savanna and humid savanna ecosystems had smaller f(BNPP) but larger interannual variability in f(BNPP), and cold desert steppes had larger f(BNPP) but smaller interannual variability. While mean f(BNPP) at a site decreased significantly with increasing mean annual temperature and precipitation across sites, no consistent temporal response of f(BNPP) with annual temperature and precipitation was found within sites. Based on these results, both geographical variability in f(BNPP) and the divergent responses of f(BNPP) with climatic variables at geographical and temporal scales should be considered in global C modeling.     

Reproductive potential and seed fate of Sclerocarya birrea subsp. caffra (marula) in the low altitude savannas of South Africa

Even though Sclerocarya birrea subsp. caffra (marula) is a well-studied, keystone tree species with high ecological, commercial and cultural value, significant gaps in our understanding of its reproductive biology exist, particularly the factors limiting fruit and seed production, seed fate and the persistence of the seed bank. Therefore, a detailed quantitative assessment of these factors was conducted at five sites in the low altitude savannas of South Africa. Sites varied with respect to fire regime, large mammals, geology and rainfall. Most sites showed male-biased secondary sex ratios and the minimum fruiting stem diameter ranged between 7.1 and 15.7 cm across sites. Sites with higher levels of disturbance (fire and large browsers) had trees producing fruit at larger minimum stem diameters than sites with lower levels of disturbance. Fruit production was highly variable between individuals, within and between sites, and from year to year. Variability in fruit production across years at one site was greater than the variability across sites in one year, indicating that drivers such as weather, insect herbivory, fire and predator numbers, which vary annually, play a greater role than more constant drivers such as mammalian herbivory, soil types or long-term rainfall. No significant relationship was found between environmental variables (rainfall and temperature) and annual fruit production, indicating a trade-off between vegetative growth and reproduction between years. Since marula fruits are large and heavy, the species relies primarily on mammalian dispersal agents such as the African elephant, which have also been shown to increase the germination rate. However, rodents also appear to play a significant role in seed dispersal. Seed predation rates tend to be highest in areas of low disturbance (no fire and no large browsers). While marula has a small persistent seed bank, recruitment appears to be reliant on the current season's fruit crop. This study provides a detailed quantitative assessment of important reproductive and seed fate vital rates for future population modelling.     

Breathing with a mouth full of eggs: respiratory consequences of mouthbrooding in cardinalfish

Mouthbrooding occurs among several groups of fishes. Although a mouth full of eggs can be expected to pose a considerable respiratory problem, to our knowledge no study has examined respiratory consequences of mouthbrooding in fishes, or how hypoxia or strenuous swimming may affect the success of this reproductive strategy. In two species of cardinalfish (Apogon fragilis and Apogon leptacanthus), from the reef at Lizard Island (Great Barrier Reef), we found that mouthbrooding significantly reduced the ability to take up oxygen at low ambient oxygen levels. While the direct energetic cost of mouthbrooding appeared insignificant at rest in well-oxygenated water, mouthbrooding significantly reduced the respiratory scope of the fishes and their capacity for sustained aerobic swimming. The males spat out their eggs in hypoxia. Interestingly, the species with the larger brood, A. fragilis, spat out the brood at a higher water [O2] than did A. leptacanthus, which had a smaller mean brood mass. Moreover, in contrast to mouthbrooding A. leptacanthus, mouthbrooding A. fragilis was unable to increase its ventilatory frequency in response to hypoxia. This suggests a trade-off situation between hypoxia tolerance and brood size. Apparently, A. fragilis has sacrificed hypoxia tolerance in favour of a large brood size to a greater extent than has A. leptacanthus.     

External tissue support and fluid–structure simulation in blood flows

The objective of this work is to address the formulation of an adequate model of the external tissue environment when studying a portion of the arterial tree with fluid–structure interaction. Whereas much work has already been accomplished concerning flow and pressure boundary conditions associated with truncations in the fluid domain, very few studies take into account the tissues surrounding the region of interest to derive adequate boundary conditions for the solid domain. In this paper, we propose to model the effect of external tissues by introducing viscoelastic support conditions along the artery wall, with two—possibly distributed—parameters that can be adjusted to mimic the response of various physiological tissues. In order to illustrate the versatility and effectiveness of our approach, we apply this strategy to perform patient-specific modeling of thoracic aortae based on clinical data, in two different cases and using a distinct fluid–structure interaction methodology for each, namely an Arbitrary Lagrangian–Eulerian (ALE) approach with prescribed inlet motion in the first case and the coupled momentum method in the second case. In both cases, the resulting simulations are quantitatively assessed by detailed comparisons with dynamic image sequences, and the model results are shown to be in very good adequacy with the data.