Weighting coefficients for the estimation of sensory threshold

This paper discusses the determ-nation of difference thresholds(ED50) by least squares procedures. A table of weights (W) tocorrect ED50 for chance probability was constructed for pairedand triangle designs. The probability (P) of a correct judgmentabove chance for the paired design is P = 2p^*–1, wherep^* is the actual proportion of correct responses. For the triangledesign, P = (3p^*–l)/2. In both designs, P was weightedby W = y²/p^*q^*, where y² is the squared ordinate of the normalcurve based on P, and q^* = 1–p^*. An example of the useof the table of weights is provided.     

Novel 20-carbonate linked prodrugs of camptothecin and 9-aminocamptothecin designed for activation by tumour-associated plasmin

The first prodrugs of camptothecin and 9-aminocamptothecin that are activated by the tumour-associated protease plasmin are reported. The tripartate prodrugs consist of a tripeptide sequence recognised by plasmin, which is linked to the 20-hydroxyl group of the camptothecins via a 1,6-elimination spacer. After selective N-protection of 9-aminocamptothecin with an Aloc group, the promoiety (tripeptide-spacer conjugate) was linked to camptothecin or 9-Aloc-9-aminocamptothecin via a 20-carbonate linkage by reacting parent drugs with the p-nitrophenyl carbonate activated promoiety in the presence of DMAP. Both prodrugs showed to be stable in buffer solution and both parent drugs were released upon incubation in the presence of plasmin. Furthermore, the prodrugs showed an average 10-fold decreased cytotoxicity with respect to their parent drugs upon incubation in seven human tumour cell lines.     

Methods for the accurate estimation of confidence intervals on protein folding phi-values

Phi-values provide an important benchmark for the comparison of experimental protein folding studies to computer simulations and theories of the folding process. Despite the growing importance of phi measurements, however, formulas to quantify the precision with which phi is measured have seen little significant discussion. Moreover, a commonly employed method for the determination of standard errors on phi estimates assumes that estimates of the changes in free energy of the transition and folded states are independent. Here we demonstrate that this assumption is usually incorrect and that this typically leads to the underestimation of phi precision. We derive an analytical expression for the precision of phi estimates (assuming linear chevron behavior) that explicitly takes this dependence into account. We also describe an alternative method that implicitly corrects for the effect. By simulating experimental chevron data, we show that both methods accurately estimate phi confidence intervals. We also explore the effects of the commonly employed techniques of calculating phi from kinetics estimated at non-zero denaturant concentrations and via the assumption of parallel chevron arms. We find that these approaches can produce significantly different estimates for phi (again, even for truly linear chevron behavior), indicating that they are not equivalent, interchangeable measures of transition state structure. Lastly, we describe a Web-based implementation of the above algorithms for general use by the protein folding community.     

The implications of variable remigration intervals for the assessment of population size in marine turtles

Sea turtles nest on sandy beaches and tend to show high fidelity to specific nesting areas, but, despite this fidelity, the inter-annual variation in nesting numbers may be large. This variation may reflect the fact that turtles do not usually nest in consecutive years. Here, theoretical models are developed in which the interval between successive nesting years (the remigration interval) reflects conditions encountered on the feeding grounds, with good feeding years leading to a reduction in the remigration interval and vice versa. These simple models produce high levels of inter-annual variation in nesting numbers with, on occasion, almost no turtles nesting in some years even when the population is large and stable. The implications for assessing the size of sea turtle populations are considered.     

Method for the estimation of a double hinge kinematic model for the trapeziometacarpal joint using MR imaging

In this paper, we propose a method to estimate the parameters of a double hinge model of the trapeziometacarpal joint (TMC) by MRI-based motion analysis. The model includes two non-orthogonal and non-intersecting rotation axes accounting for flexion–extension (F–E) and adduction–abduction (A–A). We evaluated the quality of the estimated model parameters in the prediction of the relative motion of the first metacarpal bone with respect to the trapezium. As a result, we obtained that: (a) the estimated location and orientation of the F–E and A–A axes were in agreement with previous in vitro studies, (b) the motion of the first metacarpal predicted by the 2 degrees of freedom (2DoF) model exhibits a maximum surface distance error in the range of about 2 mm and (c) four thumb postures at the boundary of the TMC range of motion are sufficient to provide a good estimation of the 2DoF TMC kinematic model and good reproducibility (～1.7 mm) of the real thumb motion at TMC level.     

CODA: a combined algorithm for predicting the structurally variable regions of protein models

CODA, an algorithm for predicting the variable regions in proteins, combines FREAD a knowledge based approach, and PETRA, which constructs the region ab initio. FREAD selects from a database of protein structure fragments with environmentally constrained substitution tables and other rule-based filters. FREAD was parameterized and tested on over 3000 loops. The average root mean square deviation ranged from 0.78 A for three residue loops to 3.5 A for eight residue loops on a nonhomologous test set. CODA clusters the predictions from the two independent programs and makes a consensus prediction that must pass a set of rule-based filters. CODA was parameterized and tested on two unrelated separate sets of structures that were nonhomologous to one another and those found in the FREAD database. The average root mean square deviation in the test set ranged from 0.76 A for three residue loops to 3.09 A for eight residue loops. CODA shows a general improvement in loop prediction over PETRA and FREAD individually. The improvement is far more marked for lengths six and upward, probably as the predictive power of PETRA becomes more important. CODA was further tested on several model structures to determine its applicability to the modeling situation. A web server of CODA is available at http://www-cryst.bioc.cam.ac.uk/~charlotte/Coda/search_coda.html.     

Between-day reliability of a method for non-invasive estimation of muscle composition

Tensiomyography is a method for valid and non-invasive estimation of skeletal muscle fibre type composition. The validity of selected temporal tensiomyographic measures has been well established recently; there is, however, no evidence regarding the method's between-day reliability. Therefore it is the aim of this paper to establish the between-day repeatability of tensiomyographic measures in three skeletal muscles. For three consecutive days, 10 healthy male volunteers (mean±SD: age 24.6 ± 3.0 years; height 177.9 ± 3.9 cm; weight 72.4 ± 5.2 kg) were examined in a supine position. Four temporal measures (delay, contraction, sustain, and half-relaxation time) and maximal amplitude were extracted from the displacement-time tensiomyogram. A reliability analysis was performed with calculations of bias, random error, coefficient of variation (CV), standard error of measurement, and intra-class correlation coefficient (ICC) with a 95% confidence interval. An analysis of ICC demonstrated excellent agreement (ICC were over 0.94 in 14 out of 15 tested parameters). However, lower CV was observed in half-relaxation time, presumably because of the specifics of the parameter definition itself. These data indicate that for the three muscles tested, tensiomyographic measurements were reproducible across consecutive test days. Furthermore, we indicated the most possible origin of the lowest reliability detected in half-relaxation time.     

Populations in variable environments: the effect of variability in a species' primary resource

Mechanistic models for herbivore populations responding to rainfall-driven pasture are used to explore the effect of temporal variability in a primary resource on the abundance and distribution of a species. If the numerical response of the herbivore to pasture is a convex function, then gains made over time intervals with above average rainfall do not compensate for losses incurred when rainfall is below average. Populations therefore fare worse when rainfall is variable compared with when rainfall is reliable. It is demonstrated that this result is independent of the distribution of rainfall. Sensitivity of a species to variability, and hence the limit to its distribution in variable environments, is directly proportional to the difference between population growth rate under ideal conditions and the estimated rate of decline as the species' resource tends to zero. When density dependence is included in the numerical response, the average abundance of a species declines with increasing variability in its primary resource. However, a model for the dynamics of pasture and rabbits (Oryctolagus cuniculus) and red foxes (Vulpes vulpes) in southern Australia, is used to illustrate that trophic interactions can reverse the effect of variability: in the absence of foxes, the mean abundance of rabbits declines with variability as expected, but in the full model the mean abundance of rabbits increases.     

Decellularization of porcine skeletal muscle extracellular matrix for the formulation of a matrix hydrogel: a preliminary study

Extracellular matrix (ECM) hydrogels are used as scaffolds to facilitate the repair and reconstruction of tissues. This study aimed to optimize the decellularization process of porcine skeletal muscle ECM and to formulate a matrix hydrogel scaffold. Five multi‐step methods (methods A–E) were used to generate acellular ECM from porcine skeletal muscle [rinsing in SDS, trypsin, ethylenediaminetetraacetic acid (EDTA), Triton X‐100 and/or sodium deoxycholate at 4–37°C]. The resulting ECM was evaluated using haematoxylin and eosin, 4‐6‐diamidino‐2‐phenylindole (DAPI) staining, and DNA quantification. Acellular matrix was dissolved in pepsin and gelled at 37°C. Hydrogel response to temperature was observed in vivo and in vitro. ECM components were assessed by Masson, Sirius red, and alcian blue staining, and total protein content. Acellular porcine skeletal muscle exhibited a uniform translucent white appearance. No intact nuclear residue was detected by haematoxylin and eosin staining, while DAPI staining showed a few nuclei in the matrixes produced by methods B, C, and D. Method A generated a gel that was too thin for gelation. However, the matrix obtained by rinsing in 0.2% trypsin/0.1% EDTA, 0.5% Triton X‐100, and 1% Triton X‐100/0.2% sodium deoxycholate was nuclei‐free and produced a viscous solution that formed a structurally stable white jelly‐like hydrogel. The residual DNA content of this solution was 49.37 ± 0.72 ng/mg, significantly less than in fresh skeletal muscle, and decreased to 19.22 ± 0.85 ng/mg after gelation (P < 0.05). The acellular matrix was rich in collagen and glycosaminoglycan, with a total protein concentration of 64.8 ± 6.9%. An acellular ECM hydrogel from porcine skeletal muscle was efficiently produced.     

Biopharmaceutical liquid formulation: a review of the science of protein stability and solubility in aqueous environments

Formulation scientists employed in the biopharmaceutical industry face the challenge of creating liquid aqueous formulations for proteins that never had evolutionary pressure to be exceptionally stable or soluble. Yet commercial products usually need a shelf life of 2 years to be economically viable. The research done in this field is dominated by physical chemists who have developed theories like preferential interaction, preferential hydration and excluded volume to explain the mechanisms for the interaction between salt, small organic molecules and proteins. This review aims to translate the research findings on protein stability and solubility produced by the physical chemists and make it accessible to formulation scientists working within the biopharmaceutical industry.     

Analysis of models for the activation and contraction of muscle

Huxley (1957) proposed a sliding filament model of muscular contraction to which Julian (1969) added equations for the activation produced by cations. Each parameter in the combined Huxley-Julian model has been varied systematically to determine its effect on the predicted twitches. The slower rate constant for Ca activation has a predominant effect on the relaxation phase of the twitch. The series elasticity and the rate constants for the making and the breaking of cross-bridges all strongly affect the contraction phase of the twitch. Further experimental work is required to determine which factor is rate limiting under a given set of conditions.Taking the Fourier transform of the twitch gives a prediction for the frequency response of the model. The predicted frequency response curves are well-fitted by those of a simple, second order system, in agreement with recent experiments (Mannard &; Stein, 1973). The parameters of the best-fitting, second-order, frequency response curves vary experimentally with mean stimulus rate. This variation probably results from a saturation at higher stimulus rates of the pXocesses for reuptake of Ca into the sarcoplasmic reticulum. The saturation of Ca reuptake, together with the saturation of the myofilaments by Ca at higher stimulus rates, can account qualitatively for the sigmoid rate-tension curves found experimentally.     

Novel method for activation of the locomotor circuitry in human

We examine the possibility for activation of the involuntary locomotion of the lower limbs by spinal electromagnetic stimulation (ES). The subject laid on the left side. The legs are supported in a gravity-neutral position by special mounting that to provide horizontal rotation in the hip, knee and ankle. ES (3 Hz and 1.56 Tesla) at the T11,-T12 vertebrae induced involuntary locomotor-like movements in the legs. The latency from the initiation of ES to the first EMG burst compoused 0.68 +/- 1.0 s and it shortened at increasing of the frequency ES from 3 Hz to 20 Hz. Thus, the spinal ES can unduce the activation of the locomotor movements in human.     

The dynamics of the rec-system in variable environments: haploid selection in a cyclical two-state environment

The dynamics of a 3-locus infinite population with non-overlapping generations and panmixia was studied. Loci are di-allelic: two loci affect fitness under cyclical symmetric haploid selection while the third one is a modifier of recombination (rec-modifier). Selection favors alternatively haplotypes AB and ab or Ab and aB. It has been proven that under alternating selection (when period of selection consists of two generations) a dominant suppressor of recombination is displaced and the allele for non-zero recombination becomes fixed within the population. For populations with inversion heterozygosity within the selective system (i.e. with zero recombination in heterozygote for rec-modifier and non-zero for homozygotes) fixation of one of the alleles (depending on the initial point) at the rec-modifier locus is predicted. For other values of recombination parameters, the behavior of the system was studied numerically. A full bifurcation picture of parameters was obtained. Many of the results related to the case of a two-generation period hold also in the case of longer period lengths.     

Median filter algorithm for estimating the threshold of detection on custom protein arrays

We constructed protein arrays according to a titration design to estimate the assay sensitivities over varying concentrations of flu vaccine and human immunoglobulin G (IgG). After imaging, we considered the problem of appropriately distinguishing background noise from foreground signal. We applied the median filter smoothing technique and estimated the differences of the observed signal compared to the smoothed signal. If the absolute value of the difference was large, the feature was easily detectable, indicating that the spot did not blend with its surrounding neighbors. After estimating the residuals, we applied thresholding algorithms to estimate the limits of detection for each assay. At sufficiently large smoothing spans, our median filter approach performed as well or better than visual inspection and two other competing analysis methods. This suggests that a median filter approach has utility in high-throughput arrays where visual inspection is impractical.     

A modified distance variable for the Hill formalism for kinetic models of muscle contraction

The distance variable of the Hill formalism for kinetic models of muscle contraction is compared to a modified distance variable. Instead of measuring the distance from a fixed point on the myosin filament to a neighboring actin, the modified variable measures the deviation of the myosin cross-bridge from its equilibrium position. Although for attached cross-bridges the two definitions are equivalent, the new variable is an index of cross-bridge conformation for cross-bridges of all states. The modified variable may be used to complement the use of the Hill variable, or to replace it. The utility of the modified variable is illustrated by an example which matches cross-bridge structures to biochemical kinetic data and to the free energy functions necessary for the design of a kinetic model.     

A modified particle swarm optimization algorithm for parameter estimation of a biological system

Background

Mathematical modeling has achieved a broad interest in the field of biology. These models represent the associations among the metabolism of the biological phenomenon with some mathematical equations such that the observed time course profile of the biological data fits the model. However, the estimation of the unknown parameters of the model is a challenging task. Many algorithms have been developed for parameter estimation, but none of them is entirely capable of finding the best solution. The purpose of this paper is to develop a method for precise estimation of parameters of a biological model.

Methods

In this paper, a novel particle swarm optimization algorithm based on a decomposition technique is developed. Then, its root mean square error is compared with simple particle swarm optimization, Iterative Unscented Kalman Filter and Simulated Annealing algorithms for two different simulation scenarios and a real data set related to the metabolism of CAD system.

Results

Our proposed algorithm results in 54.39% and 26.72% average reduction in root mean square error when applied to the simulation and experimental data, respectively.

Conclusion

The results show that the metaheuristic approaches such as the proposed method are very wise choices for finding the solution of nonlinear problems with many unknown parameters.

     

In-vitro experimental assessment of a new robust algorithm for hip joint centre estimation

Hip joint centre (HJC) localization is used in several biomedical applications, such as movement analysis and computer-assisted orthopaedic surgery.The purpose of this study was to validate in vitro a new algorithm (MC-pivoting) for HJC computation and to compare its performances with the state-of-the-art (least square approach–LSA). The MC-pivoting algorithm iteratively searches for the 3D coordinates of the point belonging to the femoral bone that, during the circumduction of the femur around the hip joint (pivoting), runs the minimum length trajectory. The algorithm was initialized with a point distribution that can be considered close to a Monte Carlo simulation sampling all around the LSA estimate.The performances of the MC-pivoting algorithm, compared with LSA, were evaluated with tests on cadavers. Dynamic reference frames were applied on both the femur and the pelvis and were tracked by an optical localizer.Results proved the algorithm accuracy (1.7 mm±1.6, 2.3—median value±quartiles), reliability (smaller upper quartiles of the errors distribution with respect to LSA) and robustness (reduction of the errors also in case of large pelvis displacements).