Discrimination criteria for apparent two-site transport models.

The medical beliefs of a people have in the past been studied principally by cultural anthropologists. The focus of these studies is usually on intrasocietal dynamics and cultural relativism—a striking orientation. However, beliefs about disease are integral to the way groups have and continue to adapt, and are thus important to both social and biological scientists. In order to study the role of medical beliefs in the adaptation of the group, a comparative approach is needed. This requires viewing these beliefs more generically, comparing their symbolic properties, and analyzing how they are used in explaining and dealing with actual occurrences of disease. The concept of a taxonomy of disease is introduced, as well as the notion of different semantic regions in the taxonomy. In the attempt to clarify the biological significance of a group's taxonomy of disease, and of its mode of operation, the ideas of uncertainty and information are employed. The significance and fruitfulness of this approach is discussed.     

Reduced kinetic models of facilitative transport

In spite of the highly complex structural dynamics of globular proteins, the processes mediated by them can usually be described in terms of relatively simple kinetic diagrams. How do complex proteins, characterized by undergoing transitions among a possibly very large number of intermediate states, exhibit functional properties that can be interpreted in terms of kinetic diagrams consisting of only a small number of states? One possible way of explaining this apparent contradiction is that, under some conditions, a reduction of the actual complete kinetic diagram that describes all of the macromolecular states and transitions takes place. In this work, we contribute with a formal basis to this interpretation, by generalizing the procedure of diagram reduction to the case of multicyclic kinetic diagrams. As an example, we apply the procedure to a complex kinetic model of facilitative transport. We develop Monte Carlo simulations to obtain the kinetic parameters of the complex model and we compare them with the ones analytically obtained from the reduced model. We confirm that, under some conditions, the kinetic behavior of the complex transporter is indistinguishable from the one of a four-state simple carrier model, derived from the former by diagram reduction. Besides introducing some novel methodological aspects, this work further contributes to the idea that, under many physiological and experimental conditions, a reduction occurs of the complete kinetic diagram that describes the dynamics of a globular protein.     

Testing transport models with substrates and reversible inhibitors

The kinetic behavior of five models for biological transport, only one of which is based on the classical carrier mechanism, is investigated. All give hyperbolic substrate saturation curves in accord with experimental observations on many systems. Several simple kinetic tests with substrates and competitive inhibitors serve to exclude or confirm proposed models. The tests involve measuring rates of efflux of radioactive substrate in the presence of (i) a competitive inhibitor outside the cell; (ii) inhibitor inside and outside; and (iii) unlabeled substrate outside. Rules for testing hypothetical mechanisms are presented in tables which may be consulted directly, disregarding the mathematical derivation.     

Testing models for transport systems dependent on periplasmic binding proteins.

A carrier model in which transport across the cytoplasmic membrane is mediated by a periplasmic binding protein (Krupka, R.M. (1992) Biochim. Biophys. Acta 1110, 1-10) is shown to account for many of the properties of these systems: (i) Michaelis-Menten kinetics; (ii) seemingly irreversible uptake; (iii) the absence of exchange transport and counter-transport; (iv) substrate half-saturation constants that in different systems may be lower or higher than the dissociation constant of the binding protein; (v) the high concentration of the binding protein in the periplasm and its weak association with the membrane component. The binding protein appears to function as a valve or rectifier that permits the substrate to enter the cell, but blocks exit in both the energized and de-energized states. The asymmetry depends on both the abruptness and the extent of the conformational change in the binding protein. Characteristically, these systems build up steep gradients across the membrane, circumstances in which such a valve might be important. In agreement with the mechanism, (a) the binding protein is missing in members of the same family of transporters that function in export of the substrate rather than import; and (b) in Gram-positive organisms, which have no periplasmic space, binding proteins function while anchored to the cytoplasmic membrane.     

Reduced kinetic models of neutral transport in the tokamak plasma

A method for constructing reduced models of neutrals transport for problems with a reduced dimension has been proposed on the basis of the kinetic equation. The case of a cylindrically symmetric plasma column, which is a good approximation for the tokamak geometry, has been thoroughly analyzed. For this geometry, the kinetic model of neutrals in the isotropic approximation is implemented using an algorithm based on energy grouping of neutrals; this algorithm for atomic hydrogen isotopes is integrated in the ASTRA code.     

Electronic data sources for kinetic models of cell signaling

Functional understanding of signaling pathways requires detailed information about the constituent molecules and their interactions. Simulations of signaling pathways therefore build upon a great deal of data from various sources. We first survey electronic data resources for cell signaling modeling and then based on the type of data representation the data sources are broadly classified into five groups. None of the data sources surveyed provide all required data in a ready-to-be-modeled fashion. We then put forward a "wish list" for the desired attributes for an ideal modeling centric database. Finally, we close with perspectives on how electronic data sources for cell signaling modeling have developed. We suggest that future directions in such data sources are largely model-driven and are hinged on interoperability of data sources.     

A single-parameter family of adjustments for fitting enzyme kinetic models to progress-curve data.

We have investigated the rapid phosphorylation of proteins in B-lymphocytes incubated with the tumour-promoting phorbol ester 12-O-tetradecanoylphorbol 13-acetate (TPA), anti-Ig and combinations of TPA and the Ca2+ ionophore ionomycin. Two-dimensional electrophoretic analysis was used to identify the proteins phosphorylated in cells preincubated with [32P]Pi. TPA induced a characteristic pattern of labelled proteins, four of which (pp85, pp76, pp66 and pp63) showed a dose-dependent incorporation of 32P on serine residues. The phosphorylation of pp63 and pp66, in particular, correlated with the mitogenic dose-response curve. Addition of the Ca2+ ionophore ionomycin to B-cells also stimulated a characteristic incorporation of 32P into proteins, which included pp63 and pp66. With combined doses of TPA and ionomycin, these two proteins show an enhanced phosphorylation, which correlated well with the synergistic enhancement of proliferation shown by this combination of agents. Protein kinase C (PKC) was partially purified from B-cells and separated into alpha and beta subtypes. The activation of both PKCs was assessed with increasing doses of TPA and concentrations of Ca2+ of 0.1 microM and 2 microM. For both forms of PKC, in particular the beta form, higher concentrations of Ca2+ shifted the dose-response curve for TPA to the left and increased the maximum activation. Anti-Ig, which stimulated B-cells by cross-linking surface immunoglobulin and causing hydrolysis of PtdIns(4,5)P2, also caused increased phosphorylation of several proteins, which again included pp63 and pp66. These data suggest that PKC, particularly the beta form, is involved in the early part of the proliferation cascade for human B-lymphocytes. It is most probably activated in a synergistic manner by the increased Ca2+ and diacylglycerol levels which result from the earlier hydrolysis of PtdIns(4,5)P2.     

Active transport of potassium by the Cecropia midgut; tracer kinetic theory and transport pool size.

1. Tracer influx kinetics have been analysed theoretically to determine the size of the transport pool with no assumptions regarding the transport pathway. 2. For a calculation of the size of the transport pool to be made, the following six conditions are required by the theory: tracer steady state attained, tissue steady state attained, Isc measures next flux, small magnitude and constant time-course of efflux, and correction for decay in pumping rate. 3. The size of the pool, SI, is given by the steady state influx, Finfinity, divided by the mixing-time constant, alpha. 4. Some experimental results are analysed by three different graphical methods, and it is shown that these three methods are equivalent. Specifically, alpha is equal to the reciprocal of the 75% mixing time, t75, divided by 1n 4 and is equal to the reciprocal of the lag time, X. 5. The tracer kinetic theory is applied to active potassium transport across the isolated short-circuited midgut: the transport meets the six conditions required by the theory. 6. The size of the transport pool of potassium in one midgut is calculated to be 80.5 muequiv./g wet weight under high-K steady-state conditions. A value as high as this suggests that the pool is intracellular.     

Electrolyte absorption by gallbladders: models of transport.

A model of electrolyte absorption by gallbladder epithelium has been presented previously on the basis of studies on gallbladders of 12 species, including fishes, frogs, toad, turtle, guinea pig, rabbit, cat and dog. This model incorporates several physiologic and morphologic characteristics common to other transporting epithelia (e.g., intestine) such as energy-dependent solute pumps, osmotically-induced water flow into the lateral intercellular space and bulk flow of fluid driven by hydrostatic pressure along the lateral space toward the basement membrane. Because the transepithelial PD across the gallbladders of each of these species was near zero under most experimental conditions, the active transport mechanism (or, “pump”) at the basolateral membrane was considered to move Na and Cl in a coupled, one-for-one manner. The carrier mechanism was postulated to have a binding site for Na and one for Cl; it would function only if both sites were filled.Gallbladders from six other species investigated more recently (including man, monkeys, goose and Necturus) have serosa-positive transepithelial PDs of 2–8 mV. The possibility was suggested that rheogenic Na transport from mucosa to serosa might account for the PD in this group of tissues and the original model of transport would be inappropriate. This review will explore the possibility that a single model of electrolyte transport accounts for the data collected on gallbladders with PDs near zero and those having significant transepithelial PDs.An important finding which helps to reconcile the experimental observations on the two groups of gallbladders was the demonstration of coupled flux of Na and Cl from the mucosal solution into the epithelial cells. It appears that this rigid coupling of Na and Cl influx accounts for the lack of a significant PD in gallbladders of those species investigated in the earlier studies, and that rheogenic Na transport may be a property common to gallbladders of all species.     

A kinetic study of mitochondrial calcium transport.

This report describes a kinetic analysis of energy-linked Ca2+ transport in rat liver mitochondria, in which a ruthenium red/EGTA [ethanedioxy-bis(ethylamine)-tetraacetic acid] quenching technique has been used to measure rates of 45Ca2+ transport. Accurately known concentrations of free 45Ca2+ were generated with Ca2+/nitrilotriacetic acids buffers for the determination of substrate/velocity relationships. The results show that the initial velocity of transport is a sigmoidal function of Ca2+ concentration (Hill coefficient = 1.7), the Km being 4 muM Ca4 at 0 degrees C and pH 7.4. These values for the Hill coefficient and the Km remain constant in the presence of up to 2 mM phosphate, but with 10 mM acetate both parameters are increased slightly. Both permeant acids increase the maximum velocity to an extent dependent on their concentration. The Ca2+-binding site(s) of the carrier contains a group ionizing at pH approximately 7.5 at 0 degrees C, which is functional in the dissociated state. The stimulatory effect of permeant acids is ascribed to their facilitating the release of Ca2+ from the carrier to the internal phase, an interpretation which is strengthened by the lack of effect of the permeant anion SCN- on Ca2+ transport. Studies on the time-course of Ca2+ uptake and of EFTA-induced Ca2+ efflux from pre-loaded mitochondria demonstrate the reversibility of the carrier in respiring mitochondria and the extent to which this property is influenced by permeant acids. These data are accommodated in a carrier mechanism based on electrophoretic transport of Ca2+ bound to pairs of interacting acidic sites.     

The use of automated tubidimetric data for the construction of kinetic models

Summary An automated tubidimetric instrument (Bioscreen) was used to observe the growth response ofListeria monocytogenes to combinations of temperature (15–30°C), hydrogen-ion (0.1–21.9 m) (equivalent pH 4.66–7.0) and NaCl concentration (0.5–9.5% w/v). Compared to traditional plate count techniques, the technique allowed many more data points to be captured and replicates to be used, with less expenditure of effort. Optical density curves were filtered (smoothed) to minimize the effect of signal noise and the mean signal from uninoculated wells was subtracted to minimize the effect of signal draft. A novel procedure for fitting growth curves to optical density data has been developed. The procedure involves the use of the logistic function and a calibration equation for fitting, in a single step, in the dimension of optical density. This approach allowed the four parameters of the logistic equation to be derived at each set of experimental conditions. A quadratic response surface was then fitted to the curve parameters using temperature, NaCl and hydrogen-ion concentration as three independent variables. Predicted time to 1000-fold increase in cell numbers compared well to predictions from predictive microbial growth equations generated in other laboratories using traditional plate counting. We propose that this technique should be further evaluated as a method for generating data for modeling the kinetics of microbial growth.Mention of brand or firm names does not constitute an endorsement by the US Department of Agriculture over others of a similar nature not mentioned.     

Robust regression of enzyme kinetic data.

A method described previously [Cornish-Bowden & Endrenyi (1981) Biochem. J. 193, 1005-1008] for fitting theoretical equations to enzyme kinetic data without prior knowledge of weights or error distribution has been tested by computer simulation. With the equations for various kinds of linear inhibition as an example, the method performed well under all of the conditions examined, giving results that were often much better than those given by widely used least-squares alternatives, and were never appreciably worse. Although equations for two-substrate kinetics were not explicitly tested, the results for inhibition equations can be generalized to include two-substrate equations because the two are formally equivalent for simulation purposes. As a check on the results with inhibition equations the method was also tested for fitting bell-shaped pH-activity profiles and gave correspondingly good results.     

Analysis and understanding of high-dimensionality data by means of multivariate data analysis

Multivariate analysis such as principal-components analysis (PCA) and partial-least-squares-discriminant analysis (PLS-DA) have been applied to peptidomics data from clinical urine samples subjected to LC/MS analysis. We show that it is possible to use these methods to get information from a complex set of clinical data. The aim of the work is to use this information as a first step in the further search for clinical biomarker data. It is possible to identify peptide-biomarker fingerprints related to disease diagnosis and progression. Further, we review clinical proteomics and pharmacogenomics data analyzed with the same multivariate approach.     

Analysis of G.F. Gause experimental time-series by means of continuous-time models

Four population dynamics models, namely Verhulst, Gompertz, Rosenzweig, and Svirezhev ones, have been used to approximate two well-known time-series of Paramecia aurelia and P. caudatum population size (Gause, 1934). The parameters are estimated for each of the models by the least-square method (with global fitting) in two different ways: with and without an additional upper bound for a parameter value. In the latter (traditional) case, when the deviations of theoretical (model) trajectories from experimental time-series have been tested for normality (Kolmogorov-Smirnov test, Shapiro-Wilk test) with zero average, and for the presence/absence of serial correlations (Durbin-Watson criteria), the best results are obtained for the Gompertz and Verhulst models. In the former, more realistic, case (when we impose an additional constraint that the parameter meaning the carrying capacity of the environment has to be greater than any element in the sample), the best results are observed for the Gompertz model. Under this constraint, the canonical technique for deviation analysis can be applied in a restricted version only.     

Useful short-range transport of mouse embryos by means of a nonfreezing technique.

The survival of mouse morulae to be implanted on the uterine wall of a recipient after storage at 0 degree C in sucrose-containing medium has shown tendencies similar to those of blastocysts developing in vitro. The pregnancy rate, as defined by implantation sites per embryos transferred, has varied from 52.9 to 77.2% and decreased depending on the duration of storage (0 to 72 h), and was lower than the rate of blastocyst formation in vitro (57.2 to 87.3%). Regarding the birth rate, 56.0 to 59.4% of implanted embryos were delivered as live pups regardless of storage duration, with the exception of controls (78.9%, 0 h). Eventually, 37.0, 32.8, or 29.9% of embryos were obtained as live pups when preserved by our system for 24, 48, or 72 hours, respectively. This viable, highly reproducible nonfreezing technique is useful for embryo preservation. Embryos were transported to evaluate the efficacy of the nonfreezing method. Mouse morulae were kept in a thermos bottle filled with ice-water and packaged in polystyrene foam. The package was transported from Kochi to Sapporo, about 1300 km, within 48 hours during which it was possible to maintain 0 degree C in the bottle and deliver to most areas in Japan. After shipping, the survival of embryos was 46.8% for development to blastocysts in vitro, and 37.1% for the pregnancy rate, with a final birth rate of 14.1%. Transport factors other than storage may have contributed to the lower birth rate; however, our system is cheaper, more convenient, and more practical than others for short-range transport.     

Evaluation of primary care in a community clinic by means of explicit process criteria.

This study reports an evaluation of care given at an urban multidisciplinary community family practice clinic. By means of an "indicator-condition" approach, the criteria and rating system developed for the Burlington Randomized Controlled Trial (BRCT) were applied to 103 randomly selected charts demonstrating 124 episodes of care given for seven specific "conditions": otitis media, hypertension, prenatal care, care of the newborn up to the age of 12 months, immunization up to the age of 24 months, depression and urinary tract infection. Overall, 83 (67%) of the episodes of care studied were rated adequate or superior. The proportion of such episodes varied from 33% for hypertension to 81% for care of the newborn. No statistically significant differences were found between these results and those of the BRCT. A total of 48 instances of inadequate care were noted, of which 21 (44%) were omissions in patient management. Inadequate preventive care and care of chronic diseases was more common than inadequate care of acute infectious diseases. The method of primary care assessment used was found to be both practical and inexpensive.     

Optimal rejection of movement artefacts from myoelectric signals by means of a wavelet filtering procedure.

In this work the problem of rejection of motion artefacts from surface myoelectric signals, recorded during dynamic contractions, is studied. In fact, the extraction of frequency parameters and the detection of muscular activation patterns can be detrimentally affected by artefacts due to the movement of the surface electrodes, particularly stressed by the dynamic conditions of the exercise performed during measurement. In order to overcome this difficulty, four different filtering procedures have been tested and compared: a high-pass filtering procedure, a moving average procedure, a moving median procedure and a new adaptive wavelet based procedure, expressly designed for this work. Orthogonal Meyer wavelets are used with the aim of obtaining both a good reconstruction and a decomposition of the signal into non-overlapping bands. The four procedures have been tested with a set of different proofs utilising both synthetic and experimentally recorded myoelectric signals. The results show that the wavelet procedure performs better than the other methods both in information preservation and in time-detection. Moreover, the features of user-independence and adaptivity to the noise level suggest a wider range of applications of the proposed algorithm.