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Immunocytochemical localization of c-erbB-2 protein in transitional cell carcinoma of the urinary bladder.

The level of expression and cellular localization of the c-erbB-2 gene product in transitional cell carcinoma of the urinary tract is controversial. Analysis of the c-erbB-2 gene structure and comparison of its expression in the same cells by Southern, Northern and immunoblotting, and by immunocytochemistry minimize the errors of interpretation inherent in one technique. Such a 'correlative study' has been performed on tumours from 82 patients. c-erbB-2 gene amplification was detected in 14 per cent of initial tumours and was associated with grade (P < 0.001). Raised levels of mRNA were seen in those tumours with increased gene copy number and in 13 per cent of the remainder. Immunoblotting detected the expected 185 kD immunoreactive protein and a 155 kD protein associated with high gene copy number. Immunocytochemistry localized c-erbB-2 immunoreactivity to the cell membrane and cytoplasm, and the latter predominated. Four antibodies to c-erbB-2 (AB-3, 21N, pAb 1, and NCL CB11) were compared on contiguous sections of the same tumour and showed the same pattern of immunoreactivity. Similarly, analyses carried out in three independent laboratories identified the same cellular localization. Membrane and cytoplasmic immunoreactivity was demonstrated in all tumours with gene amplification or increased mRNA levels and in 40 per cent of the remaining tumours. We showed that immunocytochemistry requires careful standardization of techniques and quantitation between different groups. However, despite variations in the intensity of immunoreactivity, the total number of positive cells remained constant. Therefore quantitation must be based on the number of positive cells and, ideally, their immunoreactive content relative to normal and positive tissue controls.

Biomarkers, Tumor↗

An automated method for modeling proteins on known templates using distance geometry.

We present an automated method incorporated into a software package, FOLDER, to fold a protein sequence on a given three-dimensional (3D) template. Starting with the sequence alignment of a family of homologous proteins, tertiary structures are modeled using the known 3D structure of one member of the family as a template. Homologous interatomic distances from the template are used as constraints. For nonhomologous regions in the model protein, the lower and the upper bounds for the interatomic distances are imposed by steric constraints and the globular dimensions of the template, respectively. Distance geometry is used to embed an ensemble of structures consistent with these distance bounds. Structures are selected from this ensemble based on minimal distance error criteria, after a penalty function optimization step. These structures are then refined using energy optimization methods. The method is tested by simulating the alpha-chain of horse hemoglobin using the alpha-chain of human hemoglobin as the template and by comparing the generated models with the crystal structure of the alpha-chain of horse hemoglobin. We also test the packing efficiency of this method by reconstructing the atomic positions of the interior side chains beyond C beta atoms of a protein domain from a known 3D structure. In both test cases, models retain the template constraints and any additionally imposed constraints while the packing of the interior residues is optimized with no short contacts or bond deformations. To demonstrate the use of this method in simulating structures of proteins with nonhomologous disulfides, we construct a model of murine interleukin (IL)-4 using the NMR structure of human IL-4 as the template. The resulting geometry of the nonhomologous disulfide in the model structure for murine IL-4 is consistent with standard disulfide geometry.

Algorithms↗

Simultaneous intracellular recording and calcium imaging in single neurons of hippocampal slices.

Fluorescent Ca2+ indicator dyes can be introduced into cells through the same microelectrode used for intracellular voltage recording. Simultaneous measurement of cell membrane potential and intracellular Ca2+ concentration can be very helpful in interpreting the mechanisms of Ca2+ increases. This chapter describes fluorescence image acquisition using a CCD camera and a computer program that also records a synchronized membrane potential trace. The same program allows for preliminary data analysis. More elaborate analyses can be accomplished with commercial programs. We also describe quantitative evaluations of sources of error in the use of the statistic deltaF/F as an indicator of Ca2+ concentration. Especially important errors to minimize are changes in background fluorescence and inappropriate autofluorescence corrections. Some improvement of fluorescence images of cells deep within slices may be accomplished by masking. One method is described for making a mask based on the raw fluorescence image. With another method, highly detailed cell morphologies may be conveyed by using masks based on neurobiotin injections and camera lucida drawings.

Animals↗

Characterization and correction of interpolation effects in the realignment of fMRI time series.

Subject motion in functional magnetic resonance imaging (fMRI) studies can be accurately estimated using realignment algorithms. However, residual changes in signal intensity arising from motion have been identified in the data even after realignment of the image time series. The nature of these artifacts is characterized using simulated displacements of an fMRI image and is attributed to interpolation errors introduced by the resampling inherent within realignment. A correction scheme that uses a periodic function of the estimated displacements to remove interpolation errors from the image time series on a voxel-by-voxel basis is proposed. The artifacts are investigated using a brain phantom to avoid physiological confounds. Small- and large-scale systematic displacements show that the artifacts have the same form as revealed by the simulated displacements. A randomly displaced phantom and a human subject are used to demonstrate that interpolation errors are minimized using the correction.

Algorithms↗

A model-based method for retrospective correction of geometric distortions in diffusion-weighted EPI.

The self-diffusion tensor may be calculated from several echo-planar image acquisitions preceded by different diffusion gradients. Unfortunately, these diffusion gradients cause geometric distortion that must be corrected before estimation of the tensor. In the present paper we suggest and implement a method for retrospective correction of these distortions firmly based on a physical model for the diffusion-weighted images. This method simultaneously estimates subject movement and distortion parameters by finding the set of parameters that minimizes residual error when fitting data to the diffusion tensor model. We show how this notion can be formalized as a quadratic form thereby facilitating the implementation of a rapid algorithm. In addition, we suggest models for how distortions vary with slice position and gradient direction that allow us to substantially reduce the dimensionality of the parameter space. Our results indicate that we are able to estimate both eddy current-induced distortion and subject movement directly from the data without need of any additional measurements.

Algorithms↗

Characterization of the interaction constants for the binding of two unlabelled ligands to the sites of a receptor. An experimental strategy.

The model describing the binding of three ligands to the sites of a receptor is theoretically studied in order to characterize the binding interaction between two unlabelled ligands. For this, the binding of a third labelled ligand, the affinity of which is dependent on the presence of the unlabelled ligands, must be measured in different conditions. This paper describes an experimental strategy leading to an accurate determination of the equilibrium parameters of the model. This strategy, which assumes that the model is compatible with the data, rests on the determination of the optimal experimental conditions, i.e. the choice of the ligand concentrations which minimize the error of the parameter estimates. For this purpose, a computer program which runs on a microcomputer under the MS-DOS operating system has been elaborated on the basis of the D-optimization criterion. This work shows that such a computer analysis is essential to the determination of the optimal experimental design, even when very simple biochemical systems are considered.

Ligands↗

A method for estimating the numbers of synonymous and nonsynonymous substitutions per site.

A method for estimating the numbers of synonymous (Ks) and nonsynonymous (Ka) substitutions per site is proposed. The method is based on the Li's (J. Mol. Evol. 36:96-99, 1993) and Pamilo and Bianchi's (Mol. Biol. Evol. 10:271-281, 1993) method, but a putative source of bias is solved. It is proposed that the number of synonymous substitutions that are actually transitions or transversions should be computed by separating the twofold degenerate sites into two types of sites, 2S-fold and 2V-fold, where only transitional and transversional substitutions are synonymous, respectively. Kimura's (J. Mol. Evol. 16:111-120, 1980) two-parameter correcting method for multiple substitutions at a site is then applied using the overall observed synonymous transversion frequency to estimate both the numbers of synonymous transversional (Bs) and transitional (As) substitutions per site. This approach, therefore, also minimizes stochastic errors. Computer simulations indicate that the method presented gives more accurate Ks and Ka estimates than the aforementioned methods. Furthermore, the obtention of confidence intervals for divergence estimates by computer simulation is proposed.

Animals↗

Modelling velocity profiles of rapid movements: a comparative study.

In this paper we compare 23 different models that can be used to describe the asymmetric bell-shaped velocity profiles of rapid-aimed movements. The comparison is performed with the help of an analysis-by-synthesis experiment over a database of 1052 straight lines produced by nine human subjects. For each line and for each model, a set of parameters is extracted that minimizes the error between the original and the reconstructed data. Performance analysis on the basis of the mean-square-error clearly reflects the superiority of the support-bounded lognormal model to globally describe the velocity profile characterizing rapid movements.

Biomechanical Phenomena↗

Differential effects of methylmercury on the synthesis of protein species in dorsal root ganglia of the rat.

Dorsal root ganglia from control and methylmercury (MeHg)-treated rats were incubated in vitro with 35S-methionine ant the proteins synthesized were analyzed by two-dimensional electrophoresis. The double labelling method, in which proteins of control dorsal root ganglia labelled in vitro with 3H-leucine were added to each of the two samples as an internal standard, was used to minimize unavoidable errors arising from the resolving procedure itself. The results obtained showed that the effect of MeHg on the synthesis of proteins in dorsal root ganglia was not uniform for individual protein species in the latent period of MeHg intoxication. Among 200 protein species investigated, 157 showed inhibition of synthesis close to that of the total proteins in the tissue (68% of the control). Among the remaining protein species, 20 showed real stimulation of synthesis, whereas 7 were moderately inhibited and 16 were inhibited more strongly than the total proteins in the tissue. These results suggest that the effect of MeHg on the synthetic rates for protein species in dorsal root ganglia differs with the species, and that unusual elevation or reduction of the synthesis of some protein species caused by MeHg may lead to impairment of normal nerve functions.

Animals↗

A suit calorimeter for energy balance studies on humans during heavy exercise.

A modification of the suit calorimeter originally developed in 1972 was used in combination with indirect respiratory calorimetry. The modification included increased cooling capacity of the suit by means of an increased density of cooling tubes and a variable water flow pump which permitted higher flow rates. This has made the suit calorimeter a very effective heat exchanger that could be used for studies on high energy turnover during heavy exercise. Furthermore, specially designed absorption clothing made it possible to collect any sweat produced before it evaporated, thus minimizing potential error in measuring evaporative heat loss. The suit calorimeter would seem to offer a valuable tool in the analysis of the specific thermogenic responses to dietary changes and physical activity in studies on energy and protein metabolism and their interaction in humans. It also makes it possible to perform direct calorimetric measurements in metabolic balance studies using continuous parenteral infusion since the subjects do not need to be sealed in a calorimeter chamber.

Adolescent↗

Fluorine concentration changes in human periodontally diseased tooth roots following several treatment times with citric acid.

Citric acid conditioning of exposed cementum has become an important adjunct to the clinical management of periodontal disease, and aggressive root planing is recommended to remove hypermineralized and endotoxin-laden diseased cementum. A nuclear resonance reaction technique was used to examine fluorine concentration changes subsequent to application of citric acid (pH 1.0) to the periodontal disease-exposed cementum surfaces of human tooth roots. The technique does not require the test teeth to be sectioned, thereby permitting longitudinal assessments of changes in fluorine concentration and minimizing measurement errors due to the considerable biological variation found between individuals. Initial fluorine concentrations ranged from 0.9%-2.4%, and maxima occurred within 4-6 microns of the surface, suggesting the presence of a hypermineralized layer. Within 60 sec, the citric acid had effectively removed the hypermineralized layer and the previously observed fluctuations in fluorine concentration leveled out at 0.3%-0.5%. Although the results indicated rapid removal of the hypermineralized layer and establishment of fluorine levels normally found in healthy cementum, the experimental design did not permit appraisal of potential effects upon the organic components of periodontally-exposed cementum.

Citrates↗

Effect of body weight on the volume of distribution of theophylline.

The volume of distribution (Vd) of theophylline and the relevant aminophylline loading dose (LD) are usually calculated on the basis of total body weight (TBW). In obese subjects it has been suggested that lean or ideal body weight (IBW) is the best predictor. In a sample of 40 acutely ill asthmatic patients (aged 22 to 78 yr, weighing 45 to 176 kg) we measured Vd and found that (1) it increases with TBW, (2) it cannot be accurately predicted from either TBW or IBW alone by a simple regression analysis. Power functions have been usefully applied in comparing the pharmacokinetics of animal species, including humans, with different body mass. In our sample, data were best fitted by the equation Vd = 1.29 TBW 0.74, which seems to take care of lean as well as obese patients. Results were confirmed (r = 0.89 between predicted and measured values) in a second independent sample of patients (aged 26 to 77 yr, weighing 38 to 167 kg). This helps to minimize the error in obtaining the target serum concentration of theophylline when giving a LD calculated from a predicted Vd value.

Adult↗

Geometric modeling of the human torso using cubic hermite elements.

We discuss the advantages and problems associated with fitting geometric data of the human torso obtained from magnetic resonance imaging, with high-order (bicubic Hermite) surface elements. These elements preserve derivative (C1) continuity across element boundaries and permit smooth anatomically accurate surfaces to be obtained with relatively few elements. These elements are fitted to the data with a new nonlinear fitting procedure that minimizes the error in the fit while maintaining C1 continuity with nonlinear constraints. Nonlinear Sobelov smoothing is also incorporated into this fitting scheme. The structures fitted along with their corresponding root mean-squared error, number of elements used, and number of degrees of freedom (df) per variable are: epicardium (0.91 mm, 40 elements, 142 df), left lung (1.66 mm, 80 elements, 309 df), right lung (1.69 mm, 80 elements. 309 df), skeletal muscle surface (1.67 mm, 264 elements, 1,010 df), fat layer (1.79 mm, 264 elements, 1.010 df), and the skin layer (1.43 mm, 264 elements, 1,010 df). The fitted surfaces are assembled into a combined finite element/boundary element model of the torso in which the exterior surfaces of the heart and lungs are modeled with two-dimensional boundary elements and the layers of the skeletal muscle, fat, and skin are modeled with finite elements. The skeletal muscle and fat layers are modeled with bicubic Hermite linear elements and are obtained by joining the adjacent surface elements for each layer. Applications for the torso model include the forward and inverse problems of electrocardiography, defibrillation studies, radiation dosage studies, and heat transfer studies.

Abdomen↗

Dynamics of adhesive rupture between fibroblasts and fibronectin: microplate manipulations and deterministic model.

To characterize the dynamics of cell-substrate adhesive rupture, we used a novel micromanipulation technique, in which individual fibroblasts seized on a rigid microplate were placed into contact with a fibronectin-coated flexible microplate, then pulled away. The fibronectin density (0-3000 molecules/microm2) and the pulling rate (1-10 microm/s) were controlled. The extent of the contact zone decreased to zero at a time threshold corresponding to adhesive rupture. The uniaxial force at the interface, computed from the deflection of the microplate, increased linearly with time and reached a maximum before dropping to zero. A deterministic model, focusing on the mean number of bonds between fibronectin and its membrane receptor on the cell surface, shows rapid rupture when the force reaches a critical value, in agreement with experimental observations. Increasing the ligand density and the rate of load raises the maximal force (30 200 nN), in reasonably good agreement with the model predictions. Minimization of error between experimental and simulated forces allowed identification of two physicochemical properties of the bond, i.e. its association rate constant (k(2D)on = 3 x 10(-4) microm2/s) and structural length (d = 3 nm). These results may help understand better fibroblast locomotion and interaction with the extracellular matrix.

3T3 Cells↗

Femur BMD bias associated with DPX-IQ reanalysis of DPX-acquired scan files.

Bone mineral density values calculated by DPX-IQ software reanalysis of original DPX software analyzed scans were compared at the femur region. Based on the results for 24 subjects each scanned on 12 different occasions, a significant bias at all sites--neck, Ward's triangle and trochanter--ranging from -0.7% (neck) to -2.1% (trochanter) was found. For the trochanter site 16 of the 24 subjects had significantly lower mean BMD values after DPX-IQ reanalysis, a trend also noted at the neck and Ward's triangle. Although it has been recommended that scans analyzed with DPX software do not require DPX-IQ reanalysis, our findings strongly indicate that DPX-IQ reanalysis is essential to minimize total error during follow-up BMD determinations.

Absorptiometry, Photon↗

Isotope dilution - high efficiency nebulization-ICP-MS: The coupling of accuracy and sensitivity.

If sample pretreatment, nebulization and method of calibration are suitably adapted to each other the performance of inductively coupled plasma - mass spectrometry ICP-MS can be greatly increased. High accuracy is obtained by high precision and low bias. For a given concentration higher sensitivity means higher count rates and therefore higher precision. Systematic errors are minimized by employing a definitive method of calibration. Increased sensitivity is obtained by introducing higher amounts of sample into the measurement system via high efficiency nebulizers (ultrasonic nebulizer, hydraulic-high pressure nebulizer according to Berndt and concentric high efficiency nebulizer according to Meinhard). Because this means also higher matrix effects a combination of ion chromatographic (IC-TMS) and thermal trace-matrix-separation by aerosol desolvation (T-TMS) is introduced. Isotope dilution (ID) proves to be the calibration most suitable to achieve the highest accuracy. First applications on the analysis of refractory metals (e.g. Ti, V, Nb, Ta) and non-metals (e.g. P, S, As, Se) showed recoveries of 60-105%, an imprecision of the recoveries of 2-50%, but an overall inaccuracy of only 0.1 to 4%.

Journal Article↗

Directional invariance during loading-related modulations of muscle activity: evidence for motor equivalence.

In the present study, we investigated the influence of external force manipulations on movements in different directions, while keeping the amplitude invariant. Subjects ( n=10) performed a series of cyclical anteroposterior, mediolateral, and oblique line-drawing movements (star drawing task) with their dominant limb in the horizontal plane. To dissociate kinematics from the underlying patterns of muscle activation, spring loading was applied to the forearm of the moving limb. Whereas spring loading of the arm resulted in considerable changes in the overall amount of muscle activation in the elbow and shoulder muscles, invariance was largely maintained at the kinematic level. Subjects produced the required movement directions and amplitudes of the star drawing largely successfully, irrespective of the force bias induced by the spring. These observations demonstrate motor equivalence and strengthen the notion that the spatial representation of drawing movements is encoded in the higher brain regions in a rather abstract form that is dissociated from the concrete muscle activation patterns underlying a particular movement direction. To achieve this goal, the central nervous system shifted between two or more muscle grouping strategies to overcome modulations in the interaction among posture-dependent (joint stiffness), dynamic (inertial), and elastic (spring) torque components in the joints. Spring loading induced general changes in the overall amount of EMG activity, which was largely muscle but not direction specific, presumably to represent the posture-dependent biasing force of the spring. Loading was mainly shown to increase muscle coactivation in the elbow joint. This indicates that the subjects tended to increase stiffness in the elbow to compensate for changes in the spring bias forces in order to minimize trajectory errors. Changes in muscle grouping of the shoulder antagonists were mainly a consequence of movement direction but were also affected partly by loading, presumably reflecting the influence of dynamic force components. Taken together, the results confirmed the hypothesis that changes of movement direction and direction of force in the end-effector generated specific sets of muscle grouping to overcome the dynamic requirements in the joints while keeping the kinematics largely unchanged. This suggests that directional tuning in muscle activity and changes in muscle grouping reflects the formation of appropriate internal models in the CNS that give rise to motor equivalence.

Adult↗

A hierarchical foundation for models of sensorimotor control.

Successful performance of a sensorimotor task arises from the interaction of descending commands from the brain with the intrinsic properties of the lower levels of the sensorimotor system, including the dynamic mechanical properties of muscle, the natural coordinates of somatosensory receptors, the interneuronal circuitry of the spinal cord, and computational noise in these elements. Engineering models of biological motor control often oversimplify or even ignore these lower levels because they appear to complicate an already difficult problem. We modeled three highly simplified control systems that reflect the essential attributes of the lower levels in three tasks: acquiring a target in the face of random torque-pulse perturbations, optimizing fusimotor gain for the same perturbations, and minimizing postural error versus energy consumption during low- versus high-frequency perturbations. The emergent properties of the lower levels maintained stability in the face of feedback delays, resolved redundancy in over-complete systems, and helped to estimate loads and respond to perturbations. We suggest a general hierarchical approach to modeling sensorimotor systems, which better reflects the real control problem faced by the brain, as a first step toward identifying the actual neurocomputational steps and their anatomical partitioning in the brain.

Animals↗