通过自由能的差别划分蛋白质连续结构域

结构域是蛋白质三级结构下面的结构层次 ,大多数的蛋白质都可分为若干个结构域 ,结构域的不同组合使蛋白质具有不同的三级结构并具有不同的功能。蛋白质结构域的划分在理论与应用上都具有重要意义。但目前对结构域的划分还没有一个十分理想的方法。本文通过计算去折叠自由能来实现对蛋白质结构域的划分。用此方法对 5 0种不同蛋白质序列连续的双结构域进行了分析 ,大多数蛋白质的结构域划分结果与文献报道一致 ,另外一些虽然与文献报道结果不一致 ,但比文献报道的结果更合理     

A diatom based transfer function for reconstructing sea ice concentrations in the North Atlantic

A diatom based sea ice transfer function is developed using 99 surface sediment samples from the North Atlantic and the associated modern sea ice concentrations. Canonical correspondence analysis (CCA) is applied to the species assemblages of the surface sediment samples and the association of the species with two environmental parameters, August sea surface temperature and May sea ice concentration, is assessed. The results of this analysis indicate negative correlation between sea ice and sea surface temperature and that a group of diatom species is strongly associated with sea ice, especially May sea ice concentration. The results of the CCA legitimate the development of a diatom based sea ice transfer function. The maximum likelihood method has been applied as the transfer function method, as it has been proven most suitable with this particular data set. The newly developed transfer function is then used to reconstruct May sea ice concentration in three cases, each focusing on a different time period: the Last Glacial Maximum, the Younger Dryas and the Holocene. In all three cases the transfer function produces reasonable results when compared to other paleoclimatic proxy results. This suggests that the sea ice concentration reconstructed by the diatom based sea ice transfer function is a valid and reliable method, which can be applied as a valid proxy for May sea ice concentration.     

Allosteric and related phenomena: An analysis of sigmoid and non-hyperbolic functions

The graphs of rational polynomial functions are of considerable importance in enzyme kinetics but a full analysis of the turning points and inflexions is only possible for 2 : 2 functions due to the complexity of the first and second derivatives for 3 : 3 and higher degree functions. This paper describes a simple method which can be applied to rational functions of any degree in order to discover the relationship between the coefficients necessary for the curve to have an initial sigmoid inflexion and a final inflexion (which implies a maximum in the graph). This technique is then applied to the current allosteric models. In addition, a full analysis of the 2 : 2 function with a maximum is given together with a method of separating this type of behaviour (partial substrate inhibition) from the 1 : 2 function (dead-end substrate inhibition).     

Generalized Walker-Duncan Procedure for Obtaining Maximum Likelihood Estimates of Parameters of Logistic Discriminant Function

A recursive method of obtaining the maximum likelihood estimates of the parameters of the quadratic logistic discriminant function is presented. This method is an extension of the Walker and Duncan procedure (1967) proposed for the linear logistic discriminant function in a dichotomous case. A generalization of the method to the problem of discrimination between several populations is also given in the paper. It works for both linear and quadratic logistic discriminant function. After an estimation of the parameters of the logistic function a classification can be performed. An example of application of the method to automatic diagnosis of some respiratory diseases is presented. Comparison with the standard procedures used for the estimation is done by a short simulation study.     

High fidelity epigenetic inheritance: Information theoretic model predicts threshold filling of histone modifications post replication

During cell devision, maintaining the epigenetic information encoded in histone modification patterns is crucial for survival and identity of cells. The faithful inheritance of the histone marks from the parental to the daughter strands is a puzzle, given that each strand gets only half of the parental nucleosomes. Mapping DNA replication and reconstruction of modifications to equivalent problems in communication of information, we ask how well enzymes can recover the parental modifications, if they were ideal computing machines. Studying a parameter regime where realistic enzymes can function, our analysis predicts that enzymes may implement a critical threshold filling algorithm which fills unmodified regions of length at most k. This algorithm, motivated from communication theory, is derived from the maximum à posteriori probability (MAP) decoding which identifies the most probable modification sequence based on available observations. Simulations using our method produce modification patterns similar to what has been observed in recent experiments. We also show that our results can be naturally extended to explain inheritance of spatially distinct antagonistic modifications.     

Strategy for Stabilizing Enzymes Part One: Increasing Stability of Enzymes via their Multi-Point Interaction with a Support

This review states that the covalent multi-point attachment of enzymes to a support is the most general approach to stabilize them against different denaturing conditions, namely against their inactivation caused by protein unfolding. It is suggested that the change in the wavelength of the maximum emission in fluorescence spectra of a protein, resulting from its denaturation, can be used to evaluate a priori the effectiveness of stabilization. The copolymerization method of enzyme immobilization, as the most promising approach to stabilizing enzymes, is discussed in detail.     

Frequentist properties of Bayesian posterior probabilities of phylogenetic trees under simple and complex substitution models

What does the posterior probability of a phylogenetic tree mean?This simulation study shows that Bayesian posterior probabilities have the meaning that is typically ascribed to them; the posterior probability of a tree is the probability that the tree is correct, assuming that the model is correct. At the same time, the Bayesian method can be sensitive to model misspecification, and the sensitivity of the Bayesian method appears to be greater than the sensitivity of the nonparametric bootstrap method (using maximum likelihood to estimate trees). Although the estimates of phylogeny obtained by use of the method of maximum likelihood or the Bayesian method are likely to be similar, the assessment of the uncertainty of inferred trees via either bootstrapping (for maximum likelihood estimates) or posterior probabilities (for Bayesian estimates) is not likely to be the same. We suggest that the Bayesian method be implemented with the most complex models of those currently available, as this should reduce the chance that the method will concentrate too much probability on too few trees.     

Free energy distributions in proteins.

Protein molecules in solution have a broad distribution of enthalpy states. A good approximation to the distribution function for enthalpy states can be calculated, using the maximum-entropy method, from the moments of the distribution that, in turn, are obtained from the experimental temperature dependence of the heat capacity. In the present paper, we show that the enthalpy probability distribution can then be formulated in terms of a free energy function that gives the free energy of the protein corresponding to a particular value of the enthalpy. By the location of the minima in this function, the free energy distribution graphically indicates the most probable values of the enthalpy for the protein. We find that the behavior of the free energy functions for proteins falls somewhere between two different cases: a two-state like function with two minima, the relative levels of the two states changing with temperature; and, a single-minimum function where the position of the minimum shifts to higher enthalpy values as the temperature is increased. We show that the temperature dependence of the free energy function can be expressed in terms of a central free energy distribution for a given, fixed temperature (which is most conveniently chosen as the temperature of the maximum in the heat capacity). The nature of this central free energy function for a given protein thus yields all of the thermodynamic behavior of that protein over the temperature range of the denaturation process.     

xRing—An R package to identify and measure tree-ring features using X-ray microdensity profiles

Climate influences tree-ring density and ring-density variables extracted from X-ray images have been widely used for climate reconstructions. The R package xRing was developed to identify and measure tree rings on X-ray microdensity profiles automatically. This package is available for free and it offers functions to visualize and calibrate X-ray images, to detect tree-ring borders and to identify earlywood-latewood transition using wood density variations at the inter- and the intra-ring scale. The most important functions are calibrateFilm, detectRings, correctRings, detectEwLw, and getDensity. Outputs of these functions are S3 objects, for which specific methods are provided, including plot and print. The non-linear relationship between optical density of the film and wood density is defined by the function calibrateFilm. The function detectRings detects tree rings using wood density profiles as input. This function uses the difference between local maximum and minimum values to identify tree-ring borders automatically. The correctRings function is used to call a Graphical User Interface (GUI) to visualize and to correct tree-ring borders manually. After correcting tree-ring borders, the detectEwLw function is used to compute earlywood and latewood widths by dividing rings according to relative intra-ring density changes. The getDensity function computes for each tree ring the minimum (maximum) density and the mean earlywood, latewood and whole-ring density. Finally, a list with dataframes with tree-ring width and density variables can be obtained using the function getRwls. One of the major advantages of xRing package is that requires little knowledge of R language, but at the same time it can be easily changed or adapted by experienced users.     

Immediate diagnosis in vaginal cytology using interference contrast microscopy (Nomarski).

Studying fresh aspiration material from the posterior fornix and cervix, by Interference Contrast Microscopy (Nomarski) is a good method of cytologic examination. It is shown how most cell types can be observed, just as they can be by the classical Papanicolaou staining. Normal and abnormal, even dysplastic and malignant cells can be recognized. This method is also very useful for identifying parasites, fungi and bacteria, by morphology and active movements. While encoraging the use of this method, it is advisable to compare the results with slides examined later by the Papanicolaou technique, for maximum safety of the patient.     

Rapid analytical method for the determination of 220 pesticide with their isomers by GCMS-TIC

This paper presents a cost-effective and validated multi residue modified and miniaturized method for the determination of 220 chemically different groups of pesticides and their isomers. This determination method is performed with single Quaid Gas Chromatography Mass Spectrometry -Total Ion Chromatogram GCMS-TIC. Two methods was experimented and modified with different GCMS parameters to analyses most common used pesticide and their residues in the standers solution and can be applied for real environmental samples. The results showed by single Quaid GCMS-TIC it can analyze 220 pesticides including their isomers within 49.6 min and low detection limit by using modified method 2 as described in this research. Limit of detection (LOD) was ranged from 0.78 to 14.74 ng/ml (ppb) with good separation and resolution. Limit of quantification (LOQ) was ranged between 2.34 and 44.22 ng/ml (ppb). Method 2 was more accurate, shorter, and clear separation rather than method 1. This method can be successfully applied in real environmental samples proven to be a good option for routine analysis of pesticide within the maximum residue limits (MRL) referenced to European commission especially with the most common GCMS-TIC which exists in most of labs and low income countries.     

A penalized likelihood approach for a progressive three-state model with censored and truncated data: application to AIDS

We consider the estimation of the intensity and survival functions for a continuous time progressive three-state semi-Markov model with intermittently observed data. The estimator of the intensity function is defined nonparametrically as the maximum of a penalized likelihood. We thus obtain smooth estimates of the intensity and survival functions. This approach can accommodate complex observation schemes such as truncation and interval censoring. The method is illustrated with a study of hemophiliacs infected by HIV. The intensity functions and the cumulative distribution functions for the time to infection and for the time to AIDS are estimated. Covariates can easily be incorporated into the model.     

Determination of relative age using growth increments of scales as a minimally invasive method in the tropical freshwater Apteronotus leptorhynchus

This study describes a method for the determination of relative age in a tropical teleost, the brown ghost knifefish Apteronotus leptorhynchus. This method is based on identification of the maximum number of scale circuli, which is thought to be associated with the oldest scales, and thus to be the most indicative of the age of a given fish. Relative age can be inferred by relating differences in maximum circulus counts to the average rate of circulus addition, which was estimated at 34 circuli per year in adult fish through oxytetracycline marking. This method shows high inter‐investigator reliability and has a limited effect on fish because of the low number of scales required in order to determine the maximum number of circuli with a sufficiently high confidence level. Analysis of the frequency distribution of the circulus counts revealed periodic patterns that are similar among fish, presumably reflecting the environmental life history of the individuals. Regression analysis and comparison of addition rates showed that scale circulus counts and otolith ring counts are equivalent approaches for age estimation, but scale analysis is superior because of its limited invasiveness and the lower demand in terms of technical skills and expensive instrumentation.     

Comparing different approaches for determining joint torque parameters from isovelocity dynamometer measurements

Strength, or maximum joint torque, is a fundamental factor governing human movement, and is regularly assessed for clinical and rehabilitative purposes as well as for research into human performance. This study aimed to identify the most appropriate protocol for fitting a maximum voluntary torque function to experimental joint torque data. Three participants performed maximum isometric and concentric-eccentric knee extension trials on an isovelocity dynamometer and a separate experimental protocol was used to estimate maximum knee extension angular velocity. A nine parameter maximum voluntary torque function, which included angle, angular velocity and neural inhibition effects, was fitted to the experimental torque data and three aspects of this fitting protocol were investigated. Using an independent experimental estimate of maximum knee extension angular velocity gave lower variability in the high concentric velocity region of the maximum torque function compared to using dynamometer measurements alone. A weighted root mean square difference (RMSD) score function, that forced the majority (73-92%) of experimental data beneath the maximum torque function, was found to best account for the one-sided noise in experimental torques resulting from sub-maximal effort by the participants. The suggested protocol (an appropriately weighted RMSD score function and an independent estimate of maximum knee extension angular velocity) gave a weighted RMSD of between 11 and 13 Nm (4-5% of maximum isometric torque). It is recommended that this protocol be used in generating maximum voluntary joint torque functions in all torque-based modelling of dynamic human movement.     

Maximum-entropy calculation of free energy distributions for two forms of myoglobin

The temperature dependence of the heat capacity of myoglobin depends dramatically on pH. At low pH (near 4.5), there are two weak maxima in the heat capacity at low and intermediate temperatures, respectively, whereas at high pH (near 10.7), there is one strong maximum at high temperature. Using literature data for the low-pH form (Hallerbach and Hinz, 1999) and for the high-pH form (Makhatadze and Privalov, 1995), we applied a recently developed technique (Poland, 2001d) to calculate the free energy distributions for the two forms of the protein. In this method, the temperature dependence of the heat capacity is used to calculate moments of the protein enthalpy distribution function, which in turn, using the maximum-entropy method, are used to construct the actual distribution function. The enthalpy distribution function for a protein gives the fraction of protein molecules in solution having a given value of the enthalpy, which can be interpreted as the probability that a molecule picked at random has a given enthalpy value. Given the enthalpy distribution functions at several temperatures, one can then construct a master free energy function from which the probability distributions at all temperatures can be calculated. For the high-pH form of myoglobin, the enthalpy distribution function that is obtained exhibits bimodal behavior at the temperature corresponding to the maximum in the heat capacity (Poland, 2001a), reflecting the presence of two populations of molecules (native and unfolded). For this form of myoglobin, the temperature evolution of the relative probabilities of the two populations can be obtained in detail from the master free energy function. In contrast, the enthalpy distribution function for the low-pH form of myoglobin does not show any special structure at any temperature. In this form of myoglobin the enthalpy distribution function simply exhibits a single maximum at all temperatures, with the position of the maximum increasing to higher enthalpy values as the temperature is increased, indicating that in this case there is a continuous evolution of species rather than a shift between two distinct population of molecules.     

Fundamental differences between the methods of maximum likelihood and maximum posterior probability in phylogenetics

Using a four-taxon example under a simple model of evolution, we show that the methods of maximum likelihood and maximum posterior probability (which is a Bayesian method of inference) may not arrive at the same optimal tree topology. Some patterns that are separately uninformative under the maximum likelihood method are separately informative under the Bayesian method. We also show that this difference has impact on the bootstrap frequencies and the posterior probabilities of topologies, which therefore are not necessarily approximately equal. Efron et al. (Proc. Natl. Acad. Sci. USA 93:13429-13434, 1996) stated that bootstrap frequencies can, under certain circumstances, be interpreted as posterior probabilities. This is true only if one includes a non-informative prior distribution of the possible data patterns, and most often the prior distributions are instead specified in terms of topology and branch lengths. [Bayesian inference; maximum likelihood method; Phylogeny; support.].     

Computational Intelligence and Wavelet Transform Based Metamodel for Efficient Generation of Not-Yet Simulated Waveforms

The design and verification of complex electronic systems, especially the analog and mixed-signal ones, prove to be extremely time consuming tasks, if only circuit-level simulations are involved. A significant amount of time can be saved if a cost effective solution is used for the extensive analysis of the system, under all conceivable conditions. This paper proposes a data-driven method to build fast to evaluate, but also accurate metamodels capable of generating not-yet simulated waveforms as a function of different combinations of the parameters of the system. The necessary data are obtained by early-stage simulation of an electronic control system from the automotive industry. The metamodel development is based on three key elements: a wavelet transform for waveform characterization, a genetic algorithm optimization to detect the optimal wavelet transform and to identify the most relevant decomposition coefficients, and an artificial neuronal network to derive the relevant coefficients of the wavelet transform for any new parameters combination. The resulted metamodels for three different waveform families are fully reliable. They satisfy the required key points: high accuracy (a maximum mean squared error of 7.1x10^-5 for the unity-based normalized waveforms), efficiency (fully affordable computational effort for metamodel build-up: maximum 18 minutes on a general purpose computer), and simplicity (less than 1 second for running the metamodel, the user only provides the parameters combination). The metamodels can be used for very efficient generation of new waveforms, for any possible combination of dependent parameters, offering the possibility to explore the entire design space. A wide range of possibilities becomes achievable for the user, such as: all design corners can be analyzed, possible worst-case situations can be investigated, extreme values of waveforms can be discovered, sensitivity analyses can be performed (the influence of each parameter on the output waveform).     

The Active State of Mammalian Skeletal Muscle

A new technique is proposed for computing the active state of striated muscle, based on the three component model of Fenn and Marsh (8) and of Hill (7). The method permits calculation of the time course of the active state from its peak to the time at which maximum isometric twitch tension is reached. The intormation required for the calculation can be obtained from a single muscle without moving it from its mount in the lever system. The time course of the active state proved to be a function of the length of the muscle. This length dependency led to the predictions that (a) the length at which maximum force is developed during tetanic stimulation is different from that at which it is developed during a twitch, and (b) the tetanus-twitch tension ratio is a function of length. Both predictions were verified in a series of experiments on the rat gracilis anticus muscle at 17.5°C.     

Parameter estimation and model selection for Neyman-Scott point processes

This paper proposes an approximative method for maximum likelihood estimation of parameters of Neyman-Scott and similar point processes. It is based on the point pattern resulting from forming all difference points of pairs of points in the window of observation. The intensity function of this constructed point process can be expressed in terms of second-order characteristics of the original process. This opens the way to parameter estimation, if the difference pattern is treated as a non-homogeneous Poisson process. The computational feasibility and accuracy of this approach is examined by means of simulated data. Furthermore, the method is applied to two biological data sets. For these data, various cluster process models are considered and compared with respect to their goodness-of-fit.