A method for assessing the fit of a constitutive material model to experimental stress–strain data

Higher-order polynomial functions can be used as a constitutive model to represent the mechanical behaviour of biological materials. The goal of this study was to present a method for assessing the fit of a given constitutive three-dimensional material model. Goodness of fit was assessed using multiple parameters including the root mean square error and Hotelling's T ²-test. Specifically, a polynomial model was used to characterise the stress–strain data, varying the number of model terms used (45 combinations of between 3 and 11 terms) and the manner of optimisation used to establish model coefficients (i.e. determining coefficients either by parameterisation of all data simultaneously or averaging coefficients obtained by parameterising individual data trials). This framework for model fitting helps to ensure that a given constitutive formulation provides the best characterisation of biological material mechanics.     

Recovery of the motor function of the arm with the aid of a hand exoskeleton controlled by a brain–computer interface in a patient with an extensive brain lesion

The dynamics of motor function recovery in a patient with an extensive brain lesion has been investigated during a course of neurorehabilitation assisted by a hand exoskeleton controlled by a brain–computer interface. Biomechanical analysis of the movements of the paretic arm recorded during the rehabilitation course was used for an unbiased assessment of motor function. Fifteen procedures involving hand exoskeleton control (one procedure per week) yielded the following results: (a) the velocity profile for targeted movements of the paretic hand became nearly bell-shaped; (b) the patient began to extend and abduct the hand, which was flexed and adducted at the beginning of the course; and (c) the patient started supinating the forearm, which was pronated at the beginning of the rehabilitation course. The first result is interpreted as improvement of the general level of control over the paretic hand, and the two other results are interpreted as a decrease in spasticity of the paretic hand.     

A stochastic model for the spatial distribution of species based on an aggregation–repulsion rule

The heterogeneity associated with the spatial distribution of organisms is an awkward problem in ecology because this heterogeneity directly depends on the sampling scale. To specify the scope of the influence of sampling scale on the level of species aggregation, we need data sets that entail excessive sampling costs in situ. To find a solution for this problem, we can use models to simulate patterns of organisms. These models are often very complex models that take into account heterogeneity of habitats and displacement or longevity of studied species. In this article, we introduce a new stochastic model to simulate patterns for one taxon and we want this model to be parsimonious, i.e., with few parameters and able to simulate observed patterns. This model is based on an aggregation–repulsion rule. This aggregation–repulsion rule is defined by two parameters. On a large scale, the number of aggregates present on the pattern is the first parameter. On a smaller scale, the level of aggregation–repulsion among individuals is determined by a probability distribution. These two parameters are estimated from field data set in a robust way so that the simulated patterns reflect the observed heterogeneity. We apply this model to entomological data: four Diptera families, namely the Sciaridae, Phoridae, Cecidomyiidae, and Empididae. The field data for the Phoridae family are used to simulate sampling using different trap sizes. We record changes in the coefficient of variation (C) as a function of the sampling scale, and we can suggest to ecologists emergence traps of 0.6 m², in other words a square 77 × 77 cm trap, to obtain a C value under 20%. Received: February 28, 2000 / Accepted: October 14, 2000     

A new method for the quantification of superoxide dismutase mimics with an allopurinol–xanthine oxidase–lucigenin enhanced system

Allopurinol is a prodrug converted to oxypurinol by xanthine oxidase, a process followed by an efficient enzyme inhibition. Using a lucigenin-enhanced chemiluminescence method, we found that, under alkaline conditions, superoxide radicals are produced in large amounts in the first step of the interaction between the enzyme and the inhibitor. A comparison between lucigenin and cytochrome c as final detectors revealed that only the chemiluminescence technique is able to detect the superoxide anions from allopurinol oxidation. The allopurinol–xanthine oxidase–lucigenin system can be used for the quantification of various free-radical scavengers, in particular superoxide dismutase mimics. Three manganese compounds from different structural classes [manganese(II) chloride, manganese N,N′-bis(salicylidiene)ethylenediamine chloride, and manganese(III) meso-tetrakis(N-ethylpyridinium-2-yl)porphyrin] were compared at five concentrations (0.01, 0.1, 1, 10, and 100 μM). The method is fast, 16 times more sensitive than the cytochrome c assay at pH 10.1 and could be used for in vivo investigations avoiding the lucigenin redox cycle. If the concentrations of the reagents are increased and Tween 20 is added, the method is also operative at pH 7.4.     

Sensitivity analysis of the Poisson Nernst–Planck equations: a finite element approximation for the sensitive analysis of an electrodiffusion model

Biological structures exhibiting electric potential fluctuations such as neuron and neural structures with complex geometries are modelled using an electrodiffusion or Poisson Nernst–Planck system of equations. These structures typically depend upon several parameters displaying a large degree of variation or that cannot be precisely inferred experimentally. It is crucial to understand how the mathematical model (and resulting simulations) depend on specific values of these parameters. Here we develop a rigorous approach based on the sensitivity equation for the electrodiffusion model. To illustrate the proposed methodology, we investigate the sensitivity of the electrical response of a node of Ranvier with respect to ionic diffusion coefficients and the membrane dielectric permittivity.

     

Search for critical loading condition of the spine–A meta analysis of a nonlinear viscoelastic finite element model

The relative vulnerability of spinal motion segments to different loading combinations remains unknown. The meta-analysis described here using the results of a validated L2–L3 nonlinear viscoelastic finite element model was designed to investigate the critical loading and its effect on the internal mechanics of the human lumbar spine. A Box-Behnken experimental design was used to design the magnitude of seven independent variables associated with loads, rotations and velocity of motion. Subsequently, an optimization method was used to find the primary and secondary variables that influence spine mechanical output related to facet forces, disc pressure, ligament forces, annulus matrix compressive/shear stresses and anulus fibers strain. The mechanical responses with respect to the two most-relevant variables were then regressed linearly using the response surface quadratic model. Axial force and sagittal rotation were identified as the most-relevant variables for mechanical responses. The procedure developed can be used to find the critical loading for finite element models with multi input variables. The derived meta-models can be used to predict the risk associated with various loading parameters and in setting safer load limits.     

A high-performance liquid chromatography–tandem mass spectrometric method for the determination of pharmacokinetics of ganaxolone in rat,monkey, dog and human plasma

A method for determining concentration levels of ganaxolone in rat, monkey, dog and human plasma was validated in the range of 5–1500 ng/ml using a 200-μl plasma sample volume. This validation report describes the linearity, specificity, sensitivity, reproducibility, accuracy, recovery and stability of the analytical method. The inter-day C.V. ranged from 0.5 to 9.2%, intra-day C.V. from 0.7 to 8.8% and intra-day accuracy (mean absolute percentage difference) ranged from 0.0 to 14.0% for rat, monkey, dog and human plasma. The method was used for the routine analysis of ganaxolone in rat, monkey, dog and human plasma and summary of the pharmacokinetic data are presented.     

Fish oil improves motor function,limits blood–brain barrier disruption,and reduces Mmp9 gene expression in a rat model of juvenile traumatic brain injury

The effects of an oral fish oil treatment regimen on sensorimotor, blood–brain barrier, and biochemical outcomes of traumatic brain injury (TBI) were investigated in a juvenile rat model. Seventeen-day old Long-Evans rats were given a 15 mL/kg fish oil (2.01 g/kg EPA, 1.34 g/kg DHA) or soybean oil dose via oral gavage 30 min prior to being subjected to a controlled cortical impact injury or sham surgery, followed by daily doses for seven days. Fish oil treatment resulted in less severe hindlimb deficits after TBI as assessed with the beam walk test, decreased cerebral IgG infiltration, and decreased TBI-induced expression of the Mmp9 gene one day after injury. These results indicate that fish oil improved functional outcome after TBI resulting, at least in part from decreased disruption of the blood–brain barrier through a mechanism that includes attenuation of TBI-induced expression of Mmp9.     

A novel two-step extraction method with detergent/polymer systems for primary recovery of the fusion protein endoglucanase I–hydrophobin I

Extraction systems for hydrophobically tagged proteins have been developed based on phase separation in aqueous solutions of non-ionic detergents and polymers. The systems have earlier only been applied for separation of membrane proteins. Here, we examine the partitioning and purification of the amphiphilic fusion protein endoglucanase I_core–hydrophobin I (EGI_core–HFBI) from culture filtrate originating from a Trichoderma reesei fermentation. The micelle extraction system was formed by mixing the non-ionic detergent Triton X-114 or Triton X-100 with the hydroxypropyl starch polymer, Reppal PES100. The detergent/polymer aqueous two-phase systems resulted in both better separation characteristics and increased robustness compared to cloud point extraction in a Triton X-114/water system. Separation and robustness were characterized for the parameters: temperature, protein and salt additions. In the Triton X-114/Reppal PES100 detergent/polymer system EGI_core–HFBI strongly partitioned into the micelle-rich phase with a partition coefficient (K) of 15 and was separated from hydrophilic proteins, which preferably partitioned to the polymer phase. After the primary recovery step, EGI_core–HFBI was quantitatively back-extracted (K_{EGIcore–HFBI}=150, yield=99%) into a water phase. In this second step, ethylene oxide–propylene oxide (EOPO) copolymers were added to the micelle-rich phase and temperature-induced phase separation at 55°C was performed. Total recovery of EGI_core–HFBI after the two separation steps was 90% with a volume reduction of six times. For thermolabile proteins, the back-extraction temperature could be decreased to room temperature by using a hydrophobically modified EOPO copolymer, with slightly lower yield. The addition of thermoseparating co-polymer is a novel approach to remove detergent and effectively releases the fusion protein EGI_core–HFBI into a water phase.     

A liquid chromatographic–mass spectrometric (LC–MS) method for the analysis of the bis-pyridinium oxime ICD-585 in plasma: Application in a guinea pig model

In recent animal studies, several novel oxime compounds that are better than 2-PAM as antidotes against selected organophosphate (OP) nerve agents have been identified. The purpose of this study was to develop and validate a liquid chromatographic–mass spectrometric (LC–MS) method for analysis of the bis-pyridinium oxime ICD-585 (1-(2-hydroxyiminomethylpyridinium)-3-(4-carbamoylpyridinium)-propane) in plasma and to establish the utility of the method in a guinea pig model. Calibration curves were prepared using ICD-585-spiked plasma at concentrations from 0.156 to 10 μg/ml. Curves were run over a 1-month time frame and a total of 13 (n = 13) were generated. The lower limit of quantification (LLOQ) was determined to be 0.216 μg/ml. Intra- and inter-day variability was assessed by studying precision and accuracy. For intra-day studies, data from the precision determinations indicated that the % CV's ranged from 4.28 to 14.98%. The % error in the accuracy assessments ranged from ?8.73 to 4.61%. For inter-day studies, precision data ranged from 3.53 to 13.20%. The % error in the accuracy assessments ranged from 0.39 to 13.77%. Room temperature, freeze–thaw and autosampler stability was also examined. For all 3 stability studies, the compound remained within ±15% of the initial analysis. Application of the method was demonstrated by analyzing samples from guinea pigs challenged with sarin (GB) or cyclosarin (GF) (1× LD₅₀) followed with intramuscular ICD-585 (58 μM/kg, 21.8 mg/kg). At 55 min after oxime administration, mean (±SD) plasma concentrations were 15.98 (±4.88) μg/ml and 14.57 (±3.70) μg/ml in GB- and GF-exposed animals, respectively. In summary, studies have been carried out to verify the sensitivity, precision and accuracy of the assay as well as the stability of the analyte under various conditions. The method has been demonstrated to be applicable to the analysis of plasma from nerve agent-exposed guinea pigs.     

Acoustic reflectometry for an in vitro model of a human upper airway using sinusoidal wave packets and the Ware–Aki algorithm

Acoustic reflectometry is often used for estimating the cross-sectional area of a cylindrical cavity when used in combination with an acoustic pulse. The objective of this research is to sweep a spectral bandwidth from 50 Hz to 10 kHz at steps of 50 Hz, with Gaussian sinusoidal wave packets, and to apply the Ware–Aki algorithm. In practice, not only it is difficult to generate a broad spectral bandwidth, but also robust methods are required to compensate for attenuation in the propagating wave and to eliminate a DC offset component generated in its impulse response. This paper looks at using numerical techniques to compute the impulse response and estimate the cross-sectional area as a function of an increment in the frequency response. Preliminary results show that both simulated and reconstructed cross-sectional areas for an in vitro model of a human upper airway may be estimated with an appropriate resolution, suggesting that this method is suitable for such applications.     

A coarse-grain MD (molecular dynamic) simulation of PCL–PEG and PLA–PEG aggregation as a computational model for prediction of the drug-loading efficacy of doxorubicin

Abstract

Formulating a hydrophobic drug that is water-soluble is a pharmaceutical challenge. One way is to incorporate the drug in an amphiphilic micelle composed from an aggregation of block copolymers. Design of a good nano-micelle requires many trial-and-error attempts. In this article, we developed a computational model based on a coarse-grained molecular dynamic (MD) simulation and correlated outputs with previous studies. A good correlation shows that this model reliably simulates poly-lactic acid–poly-ethylene glycol (PLA–PEG) and poly-caprolactone (PCL)–PEG aggregation in water with and without the presence of doxorubicin.

Communicated by Ramaswamy H. Sarma     

A novel spectrofluorimetric method based on a reaction with an azoisoxazoles–benzenesulfonamide derivative for determination of uranium (VI) ions in water samples

Selective fluorometric detection and determination of uranium ions is provided here using a novel fluorescent reagent, namely (E)-4-([4-hydroxynaphthalen-1-yl]diazenyl)-N-(5-methyleisoxazol-3-yl) benzenesulfonamide (U^VI reagent). The U^VI reagent offers a selective fluorescence enhancement behaviour at emission wavelength = 557 nm. The parameters affecting fluorometric detection of uranium ions, such as the pH, solvent type, ligand concentration, interaction time, and interfering ions, were investigated and adjusted. The proposed U^VI reagent can detect and determine uranium ions even at low concentrations, for which the obtained limit of detection was 0.1 ppm. Additionally, this proposed determination protocol was successfully used to detect, monitor, and determine uranium ions in actual water samples.     

Retransformation of a male sterile barnase line with the barstar gene as an efficient alternative method to identify male sterile–restorer combinations for heterosis breeding

We report in this study, an improved method for identifying male sterile–restorer combinations using the barnase–barstar system of pollination control for heterosis breeding in crop plants, as an alternative to the conventional line × tester cross method. In this strategy, a transgenic male sterile barnase line was retransformed with appropriate barstar constructs. Double transformants carrying both the barnase and barstar genes were identified and screened for their male fertility status. Using this strategy, 66–90% of fertile retransformants (restored events) were obtained in Brassica juncea using two different barstar constructs. Restored events were analysed for their pollen viability and copy number of the barstar gene. Around 90% of the restored events showed high pollen viability and ∼30% contained single copy integrations of the barstar gene. These observations were significantly different from those made in our earlier studies using line (barnase) × tester (barstar) crosses, wherein only two viable male sterile–restorer combinations were identified by screening 88 different cross-combinations. The retransformation strategy not only generated several independent restorers for a given male sterile line from a single transformation experiment but also identified potential restorers in the T₀ generation itself leading to significant savings in time, cost and labour. Single copy restored plants with high pollen viability were selfed to segregate male sterile (barnase) and restorer (barstar) lines in the T₁ progeny which could subsequently be diversified into appropriate combiners for heterosis breeding. This strategy will be particularly useful for crop plants where poor transformation frequencies and/or lengthy transformation protocols are a major limitation.