2 Hz与100 Hz刺激在诱导大鼠视皮层长持续长时程增强中的不同作用

在哺乳动物的视皮层,多种不同参数的刺激可诱导出长时程增强(long-term potentiation,LTP)现象。但关于刺激参数与持续时间长于3h的长持续LTP(long lasting LTP,L-LTP)之间关系的研究较少。本研究用3周龄的大鼠视皮层脑片标本,在Ⅳ层刺激而在Ⅱ／Ⅲ层记录场电位,待场电位稳定后施加强直刺激诱导LTP,探讨2Hz与100Hz的强直刺激在诱发持续时间长于3h的L-LTP中的作用。结果表明,多于300个脉冲不同频率的刺激可稳定地诱导出L-LTP;2Hz与100Hz的刺激诱发的L-LTP有明显不同的表达形式,100Hz刺激可诱导出较大的L-LTP;频率相同而脉冲数不同的强直刺激诱发的L-LTP有相同的表达形式。以上结果提示,不同频率的强直刺激诱发的L-LTP机制可能不同;相同频率的刺激(脉冲数不同)诱发的L-LTP可能有相同的机制。     

CD of nucleic acids: III. Calculated CD of RNAs from new A, U, G, and C transition-moment parameters

New adenine (A) and uracil (U) π → π* transition-moment parameters have been derived from a recently developed semiempirical procedure. Using conformational energy probabilities based on the Boltzmann equation, the new parameters were assigned by optimizing the calculated CD of cyclic nucleotides against measured CD. The derived A-and U-parameters (along with guanine and cytosine parameters derived previously by the same procedure) have been assessed in CD spectral calculations of some polyribonucleic acid sequences, in assumed A-class geometries. Comparisons have been made between CD spectra calculated from the newly derived parameters and those calculated from parameters obtained from a combination of crystal optical measurements and quantum-mechanical calculations. Although some spectral differences do occur, for the RNA sequences considered, no major disagreements were found in CD spectral signs and shapes, between measurements and calculations. Overall, the results indicate that the newly derived A-, U-, G-, and C-parameters show better agreement between theory and experiment than those used in previous nucleic acid CD calculations.     

A cure for the plague of parameters: constraining models of complex population dynamics with allometries

A major goal of ecology is to discover how dynamics and structure of multi-trophic ecological communities are related. This is difficult, because whole-community data are limited and typically comprise only a snapshot of a community instead of a time series of dynamics, and mathematical models of complex system dynamics have a large number of unmeasured parameters and therefore have been only tenuously related to real systems. These are related problems, because long time-series, if they were commonly available, would enable inference of parameters. The resulting ‘plague of parameters’ means most studies of multi-species population dynamics have been very theoretical. Dynamical models parametrized using physiological allometries may offer a partial cure for the plague of parameters, and these models are increasingly used in theoretical studies. However, physiological allometries cannot determine all parameters, and the models have also rarely been directly tested against data. We confronted a model of community dynamics with data from a lake community. Many important empirical patterns were reproducible as outcomes of dynamics, and were not reproducible when parameters did not follow physiological allometries. Results validate the usefulness, when parameters follow physiological allometries, of classic differential-equation models for understanding whole-community dynamics and the structure–dynamics relationship.     

Nuclease digestibility of chromatin is affected by nuclei isolation procedures

Experiments using nucleases as probes of chromatin structure take place in two stages: (1) nuclei isolation, and (2) nuclease digestion. The parameters of the nuclease digestion stage are usually strictly controlled because of nuclease sensitivity to them. However, there have been no reports on whether parameters in the nuclei isolation stage affect the subsequent nuclease digestions. We have evaluated a typical nuclei isolation technique with respect to how changes in the isolation parameters affect nuclease digestion kinetics. Our observations point out that various parameters encountered in the nuclei isolation stage have a significant effect on the subsequent nuclease digestion kinetics of DNAase I. These parameters include the concentration of cells, divalent cations and phosphatase inhibitors. The pH, concentration of NaCl and concentration of detergent had little effect. Micrococcal nuclease was relatively unaffected by changes in the nuclei isolation parameters. The importance of this report lies in the demonstration that lack of control of seemingly insignificant parameters, such as cell concentration during the nuclei isolation stage, leads to subsequent irreproducible results in the DNAase I digestion. These findings indicate that great care must be exercised in the nuclei isolation stage if reproducible work is to be performed with DNAase I.     

New hydrophilicity scale derived from high-performance liquid chromatography peptide retention data: correlation of predicted surface residues with antigenicity and X-ray-derived accessible sites

A new set of hydrophilicity high-performance liquid chromatography (HPLC) parameters is presented. These parameters were derived from the retention times of 20 model synthetic peptides, Ac-Gly-X-X-(Leu)3-(Lys)2-amide, where X was substituted with the 20 amino acids found in proteins. Since hydrophilicity parameters have been used extensively in algorithms to predict which amino acid residues are antigenic, we have compared the profiles generated by our new set of hydrophilic HPLC parameters on the same scale as nine other sets of parameters. Generally, it was found that the HPLC parameters obtained in this study correlated best with antigenicity. In addition, it was shown that a combination of the three best parameters for predicting antigenicity further improved the predictions. These predicted surface sites or, in other words, the hydrophilic, accessible, or mobile regions were then correlated to the known antigenic sites from immunological studies and accessible sites determined by X-ray crystallographic data for several proteins.     

Stereochemical quality of protein structure coordinates.

Methods have been developed to assess the stereochemical quality of any protein structure both globally and locally using various criteria. Several parameters can be derived from the coordinates of a given structure. Global parameters include the distribution of phi, psi and chi 1 torsion angles, and hydrogen bond energies. There are clear correlations between these parameters and resolution; as the resolution improves, the distribution of the parameters becomes more clustered. These features show a broad distribution about ideal values derived from high-resolution structures. Some structures have tightly clustered distributions even at relatively low resolutions, while others show abnormal scatter though the data go to high resolution. Additional indicators of local irregularity include proline phi angles, peptide bond planarities, disulfide bond lengths, and their chi 3 torsion angles. These stereochemical parameters have been used to generate measures of stereochemical quality which provide a simple guide as to the reliability of a structure, in addition to the most important measures, resolution and R-factor. The parameters used in this evaluation are not novel, and are easily calculated from structure coordinates. A program suite is currently being developed which will quickly check a given structure, highlighting unusual stereochemistry and possible errors.     

Evaluation of nitric oxide synthase activity and inhibition kinetics by chemiluminescence.

The binding affinity (K(I)) and inactivation rate (k(inact)) parameters of nitric oxide synthase (NOS) inhibitors are typically estimated by kinetic activity studies. Methods currently used in the estimation of these parameters frequently employ radiolabeled materials and require intensive sample preparation. We have devised a simple, reproducible, and sensitive method for the kinetic analysis of NOS activity and inhibition kinetics using chemiluminescence. We have used this method to characterize enzyme activity for purified murine macrophage nitric oxide synthase (NOS II). Using this method, we have also estimated the inhibitory parameters for a series of competitive antagonists and mechanism-based inactivators of NOS II. The estimated parameters are in agreement with those reported using other methods. We conclude that the chemiluminescence method can be used for kinetic studies of NOS activity and inhibition. This method represents a more efficient means for conducting kinetic studies of NOS inhibition.     

Thermodynamic and rate parameters for L-tryptophan protonation reactions

Rate and thermodynamic parameters have been obtained for the protonation reactions of the aromatic amino acidl-tryptophan using a chemical relaxation technique. These have been compared with values obtained for other aliphatic amino acids. It is shown that the proton rate parameters decrease with increasing pH. This might have biological significance.     

A new semiempirical codon substitution model based on principal component analysis of mammalian sequences

Codon substitution models have traditionally been parametric Markov models, but recently, empirical and semiempirical models also have been proposed. Parametric codon models are typically based on 61×61 rate matrices that are derived from a small number of parameters. These parameters are rooted in experience and theoretical considerations and generally show good performance but are still relatively arbitrary. We have previously used principal component analysis (PCA) on data obtained from mammalian sequence alignments to empirically identify the most relevant parameters for codon substitution models, thereby confirming some commonly used parameters but also suggesting new ones. Here, we present a new semiempirical codon substitution model that is directly based on those PCA results. The substitution rate matrix is constructed from linear combinations of the first few (the most important) principal components with the coefficients being free model parameters. Thus, the model is not only based on empirical rates but also uses the empirically determined most relevant parameters for a codon model to adjust to the particularities of individual data sets. In comparisons against established parametric and semiempirical models, the new model consistently achieves the highest likelihood values when applied to sequences of vertebrates, which include the taxonomic class where the model was trained on.     

Concentrations sériques en inhibine chez les patients souffrant de varicocèle ou d’autres pathologies testiculaires

Serum inhibin, gonadal steroids and gonadotropins have been estimated in 51 patients with either a varicocele, other testis pathologies or normal sperm, and have been compared with the sperm parameters. No significant modifications in inhibin concentrations have been observed in these patients. Moreover inhibin is not correlated with any studied parameters. In conclusion, inhibin measurement does not permit to specify the etiopathogeny of testis disorders.     

Design issues for the Michaelis-Menten model

We discuss design issues for the Michaelis-Menten model and use geometrical arguments to find optimal designs for estimating a subset of the model parameters, or a linear combination of the parameters. We propose multiple-objective optimal designs when the parameters have different levels of interest to the researcher. In addition, we compare six commonly used sequence designs in the biological sciences for estimating parameters and, propose optimal choices for the parameters for geometric designs using closed-form efficiency formulas.     

Solids removal in upflow anaerobic reactors,a review

This desk study deals with the mechanisms and parameters affecting particles separation from wastewater in mainly upflow anaerobic reactors. Despite the fact that the functioning of upflow anaerobic sludge blanket (UASB) systems depends on both physical parameters and biological processes, the physical parameters have been barely reported in the literature. The reason is that the underlying mechanisms are very complex and depend on various interrelated parameters. In addition, the lack of a serious attempt to gather the entire physical theme into one picture has resulted in just a superficial understanding of this field of science. Better understanding of the interaction and role of these parameters is essential for the development of anaerobic treatment technologies. In this study, the various parameters that might affect the solid liquid separation process by filtration through the sludge bed of a UASB have been elaborated. These parameters have been classified into (1) reactor operational conditions (temperature, organic loading rate, hydraulic retention time and upflow velocity), (2) influent characteristics (influent concentration, influent particle size and influent particle charge) and (3) sludge bed characteristics (particle size distribution, extracellular polymeric substances, and charge). The overall output of this study includes (1) a literature review, (2) structuring of this field of science, and (3) highlighting fields where research is needed.     

QSAR studies on psychotomimetic phenylalkylamines

Quantitative Structure-Activity Relationship (QSAR) studies on a series of psychotomimetic phenylalkylamines have been made using a combination of Minimum Topological Difference (MTD) method and topological methodology. The topological indices used being a pool of distance-based topological indices. The regression analyses have shown that excellent results are obtained in multiparametric model containing MTD parameters, topological indices in that quantum chemical parameters has to be introduced. The predictive power of the proposed model is discussed on the basis of cross-validation parameters.     

Model parameter uncertainties in a dual-species biofilm competition model affect ecological output parameters much stronger than morphological ones

Bacterial biofilms are complex microbial depositions on immersed interfaces that form wherever the environmental conditions sustain microbial growth. Despite their name, biofilms can develop in highly irregular structures. Recently several mathematical concepts have been introduced to model these spatially structured microbial populations. Regardless of the type of model, they all have, even for microbially relatively simple systems, many parameters which generally are known at most approximately. We investigate the effect of uncertainties in model parameters on four morphological and four ecological output parameters using a nonlinear diffusion model for a biofilm in which two species compete for a shared nutrient. To this end we conduct an extensive computer simulation experiment for two different levels of data uncertainty, three different hydrodynamic conditions, and two different scenarios of bulk substrate availability. Our results indicate that input model parameter uncertainties have a much larger effect on ecological than on morphological output parameters.     

New learning automata based algorithms for adaptation of backpropagation algorithm parameters

One popular learning algorithm for feedforward neural networks is the backpropagation (BP) algorithm which includes parameters, learning rate (eta), momentum factor (alpha) and steepness parameter (lambda). The appropriate selections of these parameters have large effects on the convergence of the algorithm. Many techniques that adaptively adjust these parameters have been developed to increase speed of convergence. In this paper, we shall present several classes of learning automata based solutions to the problem of adaptation of BP algorithm parameters. By interconnection of learning automata to the feedforward neural networks, we use learning automata scheme for adjusting the parameters eta, alpha, and lambda based on the observation of random response of the neural networks. One of the important aspects of the proposed schemes is its ability to escape from local minima with high possibility during the training period. The feasibility of proposed methods is shown through simulations on several problems.     

Gender differences in hemocyte immune parameters of bivalves: the Sydney rock oyster Saccostrea glomerata and the pearl oyster Pinctada fucata

Many authors have highlighted a high inter-individual variability in immune parameters of marine bivalves. A high number of studies have reported the impact of external factors on hemocytes immune parameters such as temperature, salinity, pollutants or pathogens. However, only a few of them considered the impact of intrinsic parameters such as sex. Therefore, the present study assessed the impact of gender on hemocytes functions on two marine bivalves. Our results led to the conclusion that the gender contributes to this inter-individual variability. When studying the impact of an environmental variable, a pathogen or a pollutant, the sex of each animal should be determined and taken into account in the analysis and interpretation of immune parameters.     

Derivation of some parameters of myoelectric signals recorded during sustained constant force isometric contractions.

Mathematical expressions are derived for some parameters of the myoelectric (ME) signal recorded during a constant force isometric contraction. The expressions are developed from a stochastic model for the motor-unit action-potential trains obtained from empirical results. The following parameters: (a) the mean rectified value, (b) the mean integrated rectified value, (c) the root-mean-square value, and (d) the power density spectrum are described as functions of contraction time and constant force of an isometric muscle contraction. The calculated parameters are compared to their corresponding empirically obtained measurements which have been reported in the literature. A discussion on the behavior of the parameters during increasing contraction time is presented. Synchronization of the motor-unit action-potential trains is shown to have a pronounced effect on the parameters of the myoelectric signal. This result should be considered when analyzing long records of myoelectric signals.     

Investigation of the structure of human coronary vasculature

Some results of a morphometric study of the parameters of coronary arteries are presented. The parameters that characterize the structure of the arterial vasculature as an optimal branching system have been calculated. Statistically reliable correlations between the diameter of the bigger of two daughter vessels in a bifurcation with the diameter of the parent vessel as well as between the diameter of the smaller daughter vessel and the asymmetry coefficient have been obtained. Differences in the structural parameters of the two types of coronary arteries that provide blood delivery and distribution have been revealed. The relationships between the lengths and diameters of the arteries of different subsystems have been obtained. It is shown that asymmetrical branching is characteristic of the coronary vasculature, and self-similar asymmetric tree-like systems may be used for its modeling.     

Parameter estimation in a stochastic model of the tubuloglomerular feedback mechanism in a rat nephron

A key parameter in the understanding of renal hemodynamics is the gain of the feedback function in the tubuloglomerular feedback mechanism. A dynamic model of autoregulation of renal blood flow and glomerular filtration rate has been extended to include a stochastic differential equations model of one of the main parameters that determines feedback gain. The model reproduces fluctuations and irregularities in the tubular pressure oscillations that the former deterministic models failed to describe. This approach assumes that the gain exhibits spontaneous erratic variations that can be explained by a variety of influences, which change over time (blood pressure, hormone levels, etc.). To estimate the key parameters of the model we have developed a new estimation method based on the oscillatory behavior of the data. The dynamics is characterized by the spectral density, which has been estimated for the observed time series, and numerically approximated for the model. The parameters have then been estimated by the least squares distance between data and model spectral densities. To evaluate the estimation procedure measurements of the proximal tubular pressure from 35 nephrons in 16 rat kidneys have been analyzed, and the parameters characterizing the gain and the delay have been estimated. There was good agreement between the estimated values, and the values obtained for the same parameters in independent, previously published experiments.     

Applications of new saturation transfer electron paramagnetic resonance methodology to the rotational dynamics of the Ca-ATPase in sarcoplasmic reticulum membranes.

The presence of small amounts of weakly immobilized probes can result in large systematic errors in the measurement of correlation times (tau r) from saturation transfer EPR spectra. However, we have recently developed experimental methodology to minimize these errors (Squier and Thomas, Biophys. J., 49:921-935). In the present study we have applied this methodology to the measurement of the rotational motion of the Ca-ATPase in sarcoplasmic reticulum. This analysis involves the estimate of tau r from line-shape parameters (spectral line-height ratios) and intensity parameters (spectral integral), coupled with digital subtractions to remove spectral components corresponding to weakly immobilized probes. We have analyzed the ST-EPR spectra of the Ca-ATPase over a range of temperatures and find that, unlike line-shape parameters, intensity parameters are little affected by the subtraction of the weakly immobilized spectral component (W). Thus, tau r values from intensity parameters are a more reliable measurement of rotational motion. As reported previously, an analysis with line-shape parameters yields a nonlinear Arrhenius plot of protein mobility. However, the plot is linear when intensity parameters or corrected spectra are used, consistent with the theory for the hydrodynamic properties of a membrane protein of unchanging size and shape in a fluid bilayer. An analysis with line-shape parameters yields different effective tau r values in different spectral regions, and these tau r values are temperature-dependent. However, correction of spectra for W yields temperature-independent tau r ratios, indicating that the motional anisotropy is temperature-independent.(ABSTRACT TRUNCATED AT 250 WORDS)