Computational fluid dynamics analysis of cyclist aerodynamics: Performance of different turbulence-modelling and boundary-layer modelling approaches

This study aims at assessing the accuracy of computational fluid dynamics (CFD) for applications in sports aerodynamics, for example for drag predictions of swimmers, cyclists or skiers, by evaluating the applied numerical modelling techniques by means of detailed validation experiments. In this study, a wind-tunnel experiment on a scale model of a cyclist (scale 1:2) is presented. Apart from three-component forces and moments, also high-resolution surface pressure measurements on the scale model’s surface, i.e. at 115 locations, are performed to provide detailed information on the flow field. These data are used to compare the performance of different turbulence-modelling techniques, such as steady Reynolds-averaged Navier–Stokes (RANS), with several k–ε and k–ω turbulence models, and unsteady large-eddy simulation (LES), and also boundary-layer modelling techniques, namely wall functions and low-Reynolds number modelling (LRNM). The commercial CFD code Fluent 6.3 is used for the simulations. The RANS shear-stress transport (SST) k–ω model shows the best overall performance, followed by the more computationally expensive LES. Furthermore, LRNM is clearly preferred over wall functions to model the boundary layer. This study showed that there are more accurate alternatives for evaluating flow around bluff bodies with CFD than the standard k–ε model combined with wall functions, which is often used in CFD studies in sports.     

Change Rates and Prevalence of a Dichotomous Variable: Simulations and Applications

A common modelling approach in public health and epidemiology divides the population under study into compartments containing persons that share the same status. Here we consider a three-state model with the compartments: A, B and Dead. States A and B may be the states of any dichotomous variable, for example, Healthy and Ill, respectively. The transitions between the states are described by change rates, which depend on calendar time and on age. So far, a rigorous mathematical calculation of the prevalence of property B has been difficult, which has limited the use of the model in epidemiology and public health. We develop a partial differential equation (PDE) that simplifies the use of the three-state model. To demonstrate the validity of the PDE, it is applied to two simulation studies, one about a hypothetical chronic disease and one about dementia in Germany. In two further applications, the PDE may provide insights into smoking behaviour of males in Germany and the knowledge about the ovulatory cycle in Egyptian women.     

A generic analytical foot rollover model for predicting translational ankle kinematics in gait simulation studies

The objective of this paper is to develop an analytical framework to representing the ankle–foot kinematics by modelling the foot as a rollover rocker, which cannot only be used as a generic tool for general gait simulation but also allows for case-specific modelling if required. Previously, the rollover models used in gait simulation have often been based on specific functions that have usually been of a simple form. In contrast, the analytical model described here is in a general form that the effective foot rollover shape can be represented by any polar function ρ=ρ(φ). Furthermore, a normalized generic foot rollover model has been established based on a normative foot rollover shape dataset of 12 normal healthy subjects. To evaluate model accuracy, the predicted ankle motions and the centre of pressure (CoP) were compared with measurement data for both subject-specific and general cases. The results demonstrated that the ankle joint motions in both vertical and horizontal directions (relative RMSE ～10%) and CoP (relative RMSE ～15% for most of the subjects) are accurately predicted over most of the stance phase (from 10% to 90% of stance). However, we found that the foot cannot be very accurately represented by a rollover model just after heel strike (HS) and just before toe off (TO), probably due to shear deformation of foot plantar tissues (ankle motion can occur without any foot rotation). The proposed foot rollover model can be used in both inverse and forward dynamics gait simulation studies and may also find applications in rehabilitation engineering.     

Digital image correlation and finite element modelling as a method to determine mechanical properties of human soft tissue in vivo

The mechanical properties of human soft tissue are crucial for impact biomechanics, rehabilitation engineering, and surgical simulation. Validation of these constitutive models using human data remains challenging and often requires the use of non-invasive imaging and inverse finite element (FE) analysis. Post-processing data from imaging methods such as tagged magnetic resonance imaging (MRI) can be challenging. Digital image correlation (DIC), however, is a relatively straightforward imaging method. DIC has been used in the past to study the planar and superficial properties of soft tissue and excised soft tissue layers. However, DIC has not been used to non-invasive study of the bulk properties of human soft tissue in vivo. Thus, the goal of this study was to assess the use of DIC in combination with FE modelling to determine the bulk material properties of human soft tissue. Indentation experiments were performed on a silicone gel soft tissue phantom. A two camera DIC setup was then used to record the 3D surface deformation. The experiment was then simulated using a FE model. The gel was modelled as Neo-Hookean hyperelastic, and the material parameters were determined by minimising the error between the experimental and FE data. The iterative FE analysis determined material parameters (μ=1.80 kPa, K=2999 kPa) that were in close agreement with parameters derived independently from regression to uniaxial compression tests (μ=1.71 kPa, K=2857 kPa). Furthermore the FE model was capable of reproducing the experimental indentor force as well as the surface deformation found (R²=0.81). It was therefore concluded that a two camera DIC configuration combined with FE modelling can be used to determine the bulk mechanical properties of materials that can be represented using hyperelastic Neo-Hookean constitutive laws.     

Statistical analysis of a dynamic model for dietary contaminant exposure

This paper is devoted to the statistical analysis of a stochastic model introduced in [P. Bertail, S. Clémençon, and J. Tressou, A storage model with random release rate for modelling exposure to food contaminants, Math. Biosci. Eng. 35 (1) (2008), pp. 35–60] for describing the phenomenon of exposure to a certain food contaminant. In this modelling, the temporal evolution of the contamination exposure is entirely determined by the accumulation phenomenon due to successive dietary intakes and the pharmacokinetics governing the elimination process inbetween intakes, in such a way that the exposure dynamic through time is described as a piecewise deterministic Markov process. Paths of the contamination exposure process are scarcely observable in practice, therefore intensive computer simulation methods are crucial for estimating the time-dependent or steady-state features of the process. Here we consider simulation estimators based on consumption and contamination data and investigate how to construct accurate bootstrap confidence intervals (CI) for certain quantities of considerable importance from the epidemiology viewpoint. Special attention is also paid to the problem of computing the probability of certain rare events related to the exposure process path arising in dietary risk analysis using multilevel splitting or importance sampling (IS) techniques. Applications of these statistical methods to a collection of data sets related to dietary methyl mercury contamination are discussed thoroughly.     

Cloning,expression, and immunogenicity of novel fusion protein of Mycobacterium tuberculosis based on ESAT-6 and truncated C-terminal fragment of HSP70

Tuberculosis (TB) remains as a major public health problem worldwide. Identification and selection of immunodominant antigens of Mycobacterium tuberculosis (MTB), capable of efficiently inducing a protective immune response is the ultimate goal of TB vaccine development studies.Accordingly, this study was designed to produce a novel M. tuberculosis fusion protein consisted of MTB ESAT-6 (early secreted antigenic target-6 kDa), as a potent immunogenic protein, fused to C-terminus of MTB HSP70 (HSP70_359–610), as an appropriate carrier and adjuvant.The constructed gene was inserted into a prokaryotic expression vector (pQE30); consequently, the recombinant fusion protein with a 6xHis-tag was successfully over expressed in Escherichia coli M15. Inclusion bodies from bacterial cell lysates were solubilized and the recombinant fusion protein was easily purified by Ni-NTA affinity chromatography under denaturing conditions followed by urea gradient dialysis. The purified and refolded protein was then applied for immunization of mice that resulted in the detection of high titers of specific antibodies, high level of IFN-γ and cell proliferation.The results of our study could confirm the capability of E6H70C fusion protein, as a potential tuberculosis vaccine candidate, for the efficient induction of specific immune responses in a mouse model. However, further investigation need to evaluate the protectivity of this recombinant protein in host model.     

Quantitative analysis of the 51Cr release cytotoxicity assay for cytotoxic lymphocytes

Using ⁵¹Cr-labelled P-815 mastocytoma cells as target cells and CS7BL/6 spleen cells sensitized against DBA/2 antigens as effector cells, it is shown that the variation in the observed specific ⁵¹Cr release over a broad range of experimental conditions can be explained on the basis of a simple physical model of the interaction process. The model assumes that a target cell can be destroyed only after contact with an effector cell, contact takes place on a random basis, one contact is sufficient, and that one effector cell can kill several targets with unchanged efficiency. The fraction of target cells destroyed (f) depends only on the incubation time (t), the number of effector cells (n) and a constant interaction probability (δ). Thus f = 1 ? e^?nδt. However, the experimental measurement, the fraction of ⁵¹Cr specifically released into the supernatant during the assay, may not be the same as the fraction of target cells destroyed because it takes considerable time for the releasable ⁵¹Cr to be released from a damaged target cell. This can be overcome experimentally by following the standard 37 °C incubation with a further incubation at 45 °C during which there are no new lytic events but all previously damaged target cells release the remainder of their releasable ⁵¹Cr. The model enables one to obtain accurate measurements of relative effector cell frequency over a broad range of experimental conditions.     

Assessing the viability of tri-trophic food chain model in designing a conservation plan: The case of dwindling Quokka population

The extinction and persistence dynamics of quokka (Setonix brachyurus) population at northern jarrah forest of Australia is investigated using mathematical modelling. Predator's management demands a comprehensive understanding of the ecological circumstances associated with predation. Predation by red foxes (Vulpes vulpes) has a significant role in reducing the native animal population. This paper mainly focuses on the extinction dynamics of quokka population and its reduction by red foxes, by qualitative and quantitative analyses of a designed tri-trophic food-chain model composing a prey (quokka), a mesopredator (red fox) and apex predator (dingo). Existence of solution are analysed and shown to be uniformly bounded. We applied the concept of basic reproduction number from epidemiology to the food chain model, to derive a condition for extinction and persistence of predator population. Global stability of the predator-free equilibrium is established by geometric approach. We use Partial Rank Correlation Coefficient (PRCC) for performing global sensitivity analysis to identify most influential model parameter responsible for quokkas prevalence and mortality. Results of numerical simulation for both deterministic and stochastic model confirms the analytical finding and support those of previous studies. The outcome of this work shows that persistence and existence of quokka depend on the demographic impacts of environmental stochasticity on its own population. Based on our results, many conservation strategies are suggested to improve the overall growth of the species. We believe that declination of red fox and the presence of dingoes are important for preserving the uniform occurrence of quokkas.     

Consistent micro, macro and state-based population modelling

A population system can be modelled using a micro model focusing on the individual entities, a macro model where the entities are aggregated into compartments, or a state-based model where each possible discrete state in which the system can exist is represented. However, the concepts, building blocks, procedural mechanisms and the time handling for these approaches are very different. For the results and conclusions from studies based on micro, macro and state-based models to be consistent (contradiction-free), a number of modelling issues must be understood and appropriate modelling procedures be applied. This paper presents a uniform approach to micro, macro and state-based population modelling so that these different types of models produce consistent results and conclusions. In particular, we demonstrate the procedures (distribution, attribute and combinatorial expansions) necessary to keep these three types of models consistent. We also show that the different time handling methods usually used in micro, macro and state-based models can be regarded as different integration methods that can be applied to any of these modelling categories. The result is free choice in selecting the modelling approach and the time handling method most appropriate for the study without distorting the results and conclusions.     

Which spatial distribution model best predicts the occurrence of dominant species in semi-arid rangeland of northern Iran?

Rangelands with more than 8000 plant species occupy nearly 54.6% of the land area of Iran and thus are accounted for a rich plant genetic storage. Mazandaran province has 378,000 ha of rangelands with high plant species richness and diversity due to its climate conditions but plants distribution is at risk because of non-principle management, land use change and as a result changing environmental factors. Vegetation management strategies can be guided by models that predict plant species distribution based on governing environmental variables. This is especially useful for the dominant species that determine ecosystem processes. In fact, modelling algorithm in each SDM determines its suitability for different ecosystems. Our aim was to compare the predictive power of a number of SDMs and to evaluate the importance of a range of environmental variables as predictors in the context of semi-arid rangeland vegetation. The selected study area, the Sarkhas rangelands (northern Iran, 36°10′ 42˝ N - 51°19′ 11˝ E), covers approximately 4358.9 ha of Mazandaran province. The efficacy of four different modelling techniques as well as Ensemble model was evaluated to predict the distribution of five dominant forage plant species (Vicia villosa, Stachys lavandulifolia, Coronilla balansae, Sanguisorba minor and Alopecurus textilis). The used models included artificial neural network (ANN), boosted regression trees (BRT), classification and regression trees (CART), and random forest (RF). Ensemble, RF and CART had the highest area under curve. The AUC obtained for Vicia villosa, Stachys lavandulifolia, Coronilla balansae, Sanguisorba minor and Alopecurus textilis, were 0.90, 0.72, 0.76, 0.69 and 0.75 respectively. Ensemble model was the model that most consistently demonstrated high predictive power across species in the rangeland context investigated here. BRT exhibited the least predictive power. An importance analysis of variables showed that soil organic C according to the CART model (0.396) and K according to the RF model (0.396) were the most important environmental variables.     

Design,characterization, and in vitro antiproliferative efficacy of gemcitabine conjugates based on carboxymethyl glucan

Gemcitabine (GEM) is widely used in clinical practice in the treatment of cancer and several other solid tumors. Nevertheless, the antitumor effect of GEM is partially prevented by some limitations including short half life, and lack of tumor localizing. Carboxymethyl glucan (CMG), a carboxymethylated derivative of β-(1-3)-glucan, shows biocompatibility and biodegradability as well as a potential anticarcinogenic effect. To enhance the antiproliferative activity of GEM, four water soluble conjugates of GEM bound to CMG via diverse amino acid linkers were designed and synthesized. ¹H NMR, FT IR, elementary analysis and RP-HPLC chromatography were employed to verify the correct achievement of the conjugates. In vitro release study indicated that conjugates presented slower release in physiological buffer (pH 7.4) than acidic buffer (pH 5.5) mimicking the acidic tumor microenvironment. Moreover, A549, HeLa and Caco-2 cancer cell lines were used to evaluate the in vitro cytotoxicity of conjugates and the results showed that binding GEM to CMG significantly enhanced antiproliferative activity of GEM on A549 cells. Therefore, these conjugates may be potentially useful as a delivery vehicle in cancer therapy and worthy of further study on structure-activity relationship and antiproliferative activity in vitro and in vivo, especially for lung tumor.     

Using simultaneous equation modeling for defining complex phenotypes

Background

Interactions between multiple biological phenotypes are difficult to model. Simultaneous equation modelling (SEM), as used in econometric modelling, may prove an effective tool for this problem. Generalized linear models were used to derive the structural equations defining the interactions between cholesterol, glucose, triglycerides and high-density lipoprotein cholesterol (HDL-C). These structural equations were then applied, using SEM, to Cohort 2 data (replicates 1–100) to estimate the phenotypic structure underlying the simulation. The goal was to determine if this empiric method of deriving structural equations for use in SEM was able to recover the simulation model better than generalized linear models.

Results

First, the underlying structural equations were estimated using generalized linear model techniques, which found strong a relationship between glucose, triglycerides and HDL-C. Using these structural equations, I used SEM to evaluate these relationships jointly. I found that a combination of the empiric structural equations and the SEM method was better at recovering the underlying simulated relationship between biologic measures than generalized linear modelling.

Conclusion

The empiric SEM procedure presented here estimated different relationships between dependent variables than generalized linear modelling. The SEM procedure using empirically developed structural equations was able to recover the underlying simulation relationship partially and thus holds promise as a technique for complex phenotype analysis. Robust methods for determining the structural equations must be developed for application of SEM to population data.

     

Cells,growth factors and bioactive surface properties in a mechanobiological model of implant healing

Interface conditions are of prime importance for implant fixation in the early post-operative period and modelling of specific biochemical interactions at implant surface is still missing. We hypothesized that updating osteoblast adhesion properties and growth factor source in an active zone located at the implant surface was relevant to model biochemical interactions of implant with its environment. We proposed an innovative set of diffusive–convective–reactive equations which relevant parameters were the cell decay factor, the cell motility and the growth factor balance.Initial comparison with histomorphometic results from a stable PMMA canine implant model provided an encouraging base to implement a numerical sensitivity analysis to evaluate the role of three types of bioactive surfaces: acid-etched titanium, coarse grit-blasted acid-etched titanium and coarse grit-blasted acid-etched titanium with RGDS peptide. We found that cell diffusion decrease (acid-etched+RGDS peptide vs. PMMA), and increase of local growth factor fraction (PMMA vs. acid-etched+RGDS peptide), significantly improved the amount of mineralized tissue on the implant surface. When the variation of structural fraction to cell motility and growth factor synthesis was investigated, an envelope pattern with an optimum was obtained but this could be exceeded for strong surface modifications and/or for high growth factor concentrations. The model also confirmed that implant bioactive properties should play a limited role to reduce heterogeneity of new-formed tissue. In conclusion, we suggested that our innovative theoretical approach was relevant to investigate implant fixation and could potentially help in reduction of implant revision.     

A calcium-induced calcium release mechanism mediated by calsequestrin

Calcium (Ca²⁺)-induced Ca²⁺ release (CICR) is widely accepted as the principal mechanism linking electrical excitation and mechanical contraction in cardiac cells. The CICR mechanism has been understood mainly based on binding of cytosolic Ca²⁺ with ryanodine receptors (RyRs) and inducing Ca²⁺ release from the sarcoplasmic reticulum (SR). However, recent experiments suggest that SR lumenal Ca²⁺ may also participate in regulating RyR gating through calsequestrin (CSQ), the SR lumenal Ca²⁺ buffer. We investigate how SR Ca²⁺ release via RyR is regulated by Ca²⁺ and calsequestrin (CSQ). First, a mathematical model of RyR kinetics is derived based on experimental evidence. We assume that the RyR has three binding sites, two cytosolic sites for Ca²⁺ activation and inactivation, and one SR lumenal site for CSQ binding. The open probability (P_o) of the RyR is found by simulation under controlled cytosolic and SR lumenal Ca²⁺. Both peak and steady-state P_o effectively increase as SR lumenal Ca²⁺ increases. Second, we incorporate the RyR model into a CICR model that has both a diadic space and the junctional SR (jSR). At low jSR Ca²⁺ loads, CSQs are more likely to bind with the RyR and act to inhibit jSR Ca²⁺ release, while at high SR loads CSQs are more likely to detach from the RyR, thereby increasing jSR Ca²⁺ release. Furthermore, this CICR model produces a nonlinear relationship between fractional jSR Ca²⁺ release and jSR load. These findings agree with experimental observations in lipid bilayers and cardiac myocytes.     

Elucidating cytochrome C release from mitochondria: insights from an in silico three-dimensional model

Mitochondrial regulation of apoptosis depends on the programmed release of proapoptotic proteins such as cytochrome c (Cyt c) through the outer mitochondrial membrane (OMM). Although a few key processes involved in this release have been identified, including the liberation of inner membrane-bound Cyt c and formation of diffusible pores on the OMM, other details like the transport of Cyt c within complex mitochondrial compartments, e.g., the cristae and crista junctions, are not yet fully understood (to our knowledge). In particular, a remodeling of the inner mitochondrial membrane accompanying apoptosis seen in a few studies, in which crista junctions widen, has been hypothesized to be a necessary step in the Cyt c release. Using a three-dimensional spatial modeling of mitochondrial crista and the crista junction, model simulations and analysis illustrated how the interplay among solubilization of Cyt c, fast diffusion of Cyt c, and OMM permeabilization gives rise to the observed experimental release profile. Importantly, the widening of the crista junction was found to have a negligible effect on the transport of free Cyt c from cristae. Finally, model simulations showed that increasing the fraction of free/loosely-bound Cyt c can sensitize the cell to apoptotic stimuli in a threshold manner, which may explain increased sensitivity to cell death associated with aging.     

Antisickling properties of divanilloylquinic acids isolated from Fagara zanthoxyloides Lam. (Rutaceae)

Fagara zanthoxyloides Lam. (syn. Zanthoxylum zanthoxyloides) (Rutaceae) is the most cited Fagara species for the treatment and the prevention of sickle cell disease crisis. Sickle cell anemia (SCA) is a public health problem in many countries particularly in Africa. The present study was designed to evaluate the antisickling properties of three isomeric divanilloylquinic acids (3,4-O-divanilloylquinic acid or burkinabin A; 3,5-O-divanilloylquinic acid or burkinabin B and 4,5-O-divanilloylquinic acid or burkinabin C) identified previously by LC/MS/NMR analysis in the root bark of F. zanthoxyloides [Ouattara et al., 2004. LC/MS/NMR analysis of isomeric divanilloylquinic acids from the root bark of Fagara zanthoxyloides Lam. Phytochemistry 65, 1145–1151].The three isomers showed interesting antisickling properties which increased from burkinabins A to C.     

Assessing the In Vitro Drug Release from Lipid-Core Nanocapsules: a New Strategy Combining Dialysis Sac and a Continuous-Flow System

The in vitro assessment of drug release from polymeric nanocapsules suspensions is one of the most studied parameters in the development of drug-loaded nanoparticles. Nevertheless, official methods for the evaluation of drug release from submicrometric carriers are not available. In this work, a new approach to assess the in vitro drug release profile from drug-loaded lipid-core nanocapsules (LNC) was proposed. A continuous-flow system (open system) was designed to evaluate the in vitro drug release profiles from different LNC formulations containing prednisolone or clobetasol propionate (LNC-CP) as drug model (LNC-PD) using a homemade apparatus. The release medium was constantly renewed throughout the experiment. A dialysis bag containing 5 mL of formulation (0.5 mg mL⁻¹) was maintained inside the apparatus, under magnetic stirring and controlled temperature (37°C). In parallel, studies based on the conventional dialysis sac technique (closed system) were performed. It was possible to discriminate the in vitro drug release profile of different formulations using the open system. The proposed strategy improved the sink condition, by constantly renewing the release medium, thus maintaining the drug concentration farther from the saturated concentration in the release medium. Moreover, problems due to sampling errors can be easily overcome using this semi-automated system, since the collection is done automatically without interference from the analyst. The system proposed in this paper brings important methodological and analytical advantages, becoming a promising prototype semi-automated apparatus for performing in vitro drug release studies from drug-loaded lipid-core nanocapsules and other related nanoparticle drug delivery systems.KEY WORDS: dialysis sac technique, flow-through cell apparatus, in vitro drug release, lipid-core nanocapsules, sink condition