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PubMed2006

Bohmian mechanics with complex action: a new trajectory-based formulation of quantum mechanics.

In recent years there has been a resurgence of interest in Bohmian mechanics as a numerical tool because of its local dynamics, which suggest the possibility of significant computational advantages for the simulation of large quantum systems. However, closer inspection of the Bohmian formulation reveals that the nonlocality of quantum mechanics has not disappeared-it has simply been swept under the rug into the quantum force. In this paper we present a new formulation of Bohmian mechanics in which the quantum action, S, is taken to be complex. This leads to a single equation for complex S, and ultimately complex x and p but there is a reward for this complexification-a significantly higher degree of localization. The quantum force in the new approach vanishes for Gaussian wave packet dynamics, and its effect on barrier tunneling processes is orders of magnitude lower than that of the classical force. In fact, the current method is shown to be a rigorous extension of generalized Gaussian wave packet dynamics to give exact quantum mechanics. We demonstrate tunneling probabilities that are in virtually perfect agreement with the exact quantum mechanics down to 10(-7) calculated from strictly localized quantum trajectories that do not communicate with their neighbors. The new formulation may have significant implications for fundamental quantum mechanics, ranging from the interpretation of non-locality to measures of quantum complexity.

Journal Article↗

PubMed1998

Step-wise DNA relaxation and decatenation by NaeI-43K.

Nae I protein was originally isolated for its restriction endonuclease properties. Nae I was later discovered to either relax or cleave supercoiled DNA, depending upon whether Nae I position 43 contains a lysine (43K) or leucine (43L) respectively. Nae I-43K DNA relaxation activity appears to be the product of coupling separate endonuclease and ligase domains within the same polypeptide. Whereas Nae I relaxes supercoiled DNA like a topoisomerase, even forming a transient covalent intermediate with the substrate DNA, Nae I shows no obvious sequence similarity to the topoisomerases. To further characterize the topoisomerase activity of Nae I, we report here that Nae I-43K changes the linking number of a single negatively supercoiled topoisomer of pBR322 by units of one and therefore is a type I topoisomerase. Positively supercoiled pBR322 was resistant to Nae I-43K. At low salt concentration Nae I-43K was processive; non-saturating amounts of enzyme relaxed a fraction of the DNA. At high salt concentration the same non-saturating amounts of Nae I-43K partially relaxed all the DNA in a step-wise fashion to give a Gaussian distribution of topoisomers, demonstrating a switch from a processive to a distributive mode of action. Nae I-43K decatenated kinetoplast DNA containing nicked circles, implying that Nae I-43K can cleave opposite a nick. The products of the reaction are decatenated nicked circles under both processive and distributive conditions. The behavior of Nae I-43K is consistent with that of a prokaryotic type I topoisomerase.

DNA Topoisomerases, Type I↗

PubMed1993

Median method for detecting endogenous event-related brain potentials.

Most studies of event-related brain potentials (ERPs) use the averaging method. This procedure is assumed to increase signal/noise ratio in proportion to the square root of the number of trials if the signal is invariant and the noise is stationary. In addition, the averaged value is the appropriate measure of central tendency if the measurements have a Gaussian distribution. For endogenous ERPs, however, application of the averaging method encounters 3 serious problems. First, the invariance of signal cannot always be assumed because the endogenous signal reflects psychological processes which may be missing in some trials. Secondly, the Gaussian distribution cannot be assumed when a small number of trials is averaged. Thirdly, averaging a limited number of trials is sensitive to inclusion of occasional, non-random, noise. The characteristics of the median ERP can address all 3 problems. These characteristics are demonstrated by an original equation.

Brain↗

PubMed2005

Dynamic changes in the length distribution of actin filaments during polymerization can be modulated by barbed end capping proteins.

During actin polymerization, it has been theorized that the actin filament length distribution initially grows in the form of a Gaussian before converting to produce that of an exponential. However, it has been difficult to demonstrate this experimentally. In this study, we use modern fluorescence microscopy techniques to observe the changing actin filament length distribution during and subsequent to the polymerization process. Nucleated actin filament growth using barbed end capping proteins (gelsolin and erythrocyte capping protein) leads to Gaussian length distributions that are relatively stable. As predicted, nucleated actin filament growth using actin/spectrin complexes follows a similar process until polymerization reaches equilibrium whereafter the Gaussian length distribution rapidly converts to that of an exponential. This study provides direct confirmation of the original theories for the mode of actin polymerization but raises doubts regarding the mechanism of the length distribution conversion from Gaussian to exponential.

Actin Depolymerizing Factors↗

PubMed1998

Quantification of interstitial lung abnormalities with chest radiography: comparison of radiographic index and fractal dimension.

RATIONALE AND OBJECTIVES: The authors performed this study to evaluate two physical measures used for quantifying interstitial lung abnormalities on chest radiographs: the normalized radiographic index (RI) and the fractal dimension (FD). MATERIALS AND METHODS: The RI and FD were obtained from 50 regions of interest (ROIs) in lungs with mild interstitial abnormalities, 50 ROIs in lungs with severe interstitial abnormalities, and 50 ROIs in normal lungs. The RI was defined as the normalized percentage area of extracted opacities in selected ROIs. FD was calculated with a box-counting algorithm. To extract linear opacities selectively, the authors processed ROIs with four-directional Laplacian-Gaussian filtering and binarization, linear opacity judgment (LOJ), and linear opacity subtraction (LOS). The usefulness of the physical measures for quantifying interstitial lung abnormalities was evaluated with receiver operating characteristic analysis. RESULTS: In normal and mild abnormality groups, observer performance with the RI was worse with LOJ images (area under the receiver operating characteristic curve [Az] = .812 +/- .042) than with LOS images (Az = .912 +/- .028, P < .05), and performance with FD was better with LOJ images (Az = .867 +/- .037) than with LOS images (Az = .750 +/- .048, P < .05). In the normal and severe abnormality groups, performance with RI and FD was better with LOJ images (RI: Az = .992 +/- .007; FD: Az = .968 +/- .016) than with LOS images (RI: Az = .883 +/- .034, P < .001; FD: Az = .767 +/- .047, P < .0001). CONCLUSION: The RI is considered to reflect the sensitivity in the detection of interstitial lung abnormalities on chest radiographs. Conversely, the FD is considered to reflect specifically the linear opacities processed with LOJ.

Algorithms↗

PubMed2006

Switch and maintenance of task set in schizophrenia.

Task set maintenance and switching deficits are robust in schizophrenia. However, little is known about how these constructs are related to one another. The development of an improved understanding of set switching and maintenance deficits in schizophrenia requires that these constructs be explicated in terms of elementary cognitive processes rather than grouped into broad psychological concepts like executive functioning. A relevant dichotomy has been proposed in which sensory and perceptual ("attentional") processes are distinguished from decisional ("intentional") processes in task maintenance and switching; however, the contributions these processes make to performance deficits in schizophrenia is not known. In the present study, 30 participants with schizophrenia and 27 healthy comparisons completed a cued attentional set switching task. In addition to analyses of mean response times, the contributions of attentional and intentional processes to task performance were estimated using an ex-Gaussian distributional analysis. Schizophrenia was associated with a set maintenance deficit that was accounted for by an attentional, rather than intentional, dysfunction. Both groups showed significant switch costs that could be attributed to attentional processes, but there was no evidence for an attentional set switching deficit in schizophrenia. The findings suggest that set switching and set maintenance may reflect distinct cognitive deficits in schizophrenia and that they may be associated with unique information processing mechanisms.

Adolescent↗

PubMed2001

Computerized classification of interstitial lung abnormalities on chest radiographs with normalized radiographic index and normalized fractal dimension.

OBJECTIVE: To evaluate the performance of two kinds of physical measures, the normalized radiographic index (R) and the normalized fractal dimension (F), for computerized classification of interstitial lung abnormalities on chest radiographs. METHODS AND MATERIAL: The values of R were obtained as the normalized percent area of extracted opacities in selected regions of interest (ROIs). The values of F were calculated with a box-counting algorithm and then normalized. To extract linear opacities on chest radiographs selectively, we processed ROIs by four-directional Laplacian-Gaussian filtering and binarization (4LG/B), linear opacity judgment (LOJ), and linear opacity subtraction (LOS). We used the ROIs of 50 mild and 50 severe interstitial lung abnormalities. In both groups, all cases were divided into H (n=21, honeycombing opacities were found to be dominant) and Non-H (n=79, abnormal opacities were found, but these were excluded from H). We obtained three types of normalized physical measures of R and F in one ROI from 4LG/B, LOJ, and LOS images, and the combined indices, R(COM) and F(COM) were calculated. RESULTS: The values of F(LOJ) could differentiate H from Non-H in the mild-and the severe-abnormality group. However, all Rs could not differentiate H from Non-H in the severe-abnormality group. The combined indices of both R and F could differentiate H from Non-H in the mild-abnormality group; however, these could not differentiate H from Non-H in the severe-abnormality group. CONCLUSION: The values of F(LOJ) seem to be useful in the classification of interstitial lung abnormalities on chest radiographs.

Fractals↗

PubMed2005

Evaluating and monitoring the packing behavior of process-scale chromatography columns.

The packing characteristics of process-scale chromatography columns were evaluated using the responses to conductivity-based pulse and step inputs derived from tracer experiments and in-process transitions (i.e. column equilibration and regeneration steps). Characteristics of the measured residence time distributions (RTDs) were quantified by statistical moments and using the equations derived from the Gaussian model. The first and second moments calculated from in-process step transitions for multiple runs were in good agreement with those moments calculated from the pulse-input experiments conducted immediately after column packing. This indicates that most of the time the bed behavior at the time of packing is consistent with that at the time of operation. Due to the significant resistance to protein mass transfer inside the particles, estimated plate heights for protein solutes are expected to be much greater than those observed from the experiments using saltbased tracers. Thus, the column efficiency derived from salt-based experiments can be a useful measure of packing consistency rather than a significant parameter influencing the outcome of protein separations.

Chromatography↗

PubMed2006

Likelihood ratio, optimal decision rules, and correct response probabilities in a signal detection theoretic, equal-variance Gaussian model of the observer in the 4IAX paradigm.

This article provides a synthetic account of the likelihood ratio, optimal decision rules, and correct response probabilities in a signal detection theoretic model of the observer in the dual-pair comparison, or four-interval AX (4IAX), paradigm. The model assumes a static sampling process, resulting in four, equal-variance normally distributed (i.e., Gaussian) observations on each trial First, a likelihood ratio equation allowing for an arbitrary degree of correlation between observations is provided. Specific solutions for the cases of independent and highly correlated observations are then derived. It is shown that these solutions, and the associated decision rules, correspond to those provided independently in earlier publications. A modified 4IAX paradigm involving, as a standard, an additional stimulus (C) located medially between the A and the B stimuli is also considered. It is shown that the optimal (static, equal-variance, Gaussian) decision model for this paradigm is unaffected by correlation between observations and is equivalent to the standard 4IAX with highly correlated observations. Finally, we consider how, under the considered (static, equal-variance, Gaussian) model, the proportion of correct responses in the different versions of the 4IAX paradigm is related to d', and a solution for the case of independent observations is provided.

Decision Making↗

PubMed2007

A nonlinear latent class model for joint analysis of multivariate longitudinal data and a binary outcome.

We consider a joint model for exploring association between several correlated longitudinal markers and a clinical event. A nonlinear growth mixture model exhibits the different latent classes of evolution of the latent quantity underlying the correlated longitudinal markers and a logistic regression models the probability of occurence of the clinical event according to the latent classes. By introducing a flexible nonlinear transformation including parameters to be estimated between each marker and the latent process, the model also deals with non-Gaussian continuous markers. Through an application on cognitive ageing, the two advantages of the model are underlined: (1) the latent profiles of evolution associated with the clinical event are described including covariate effects in the longitudinal model but also in the probability of class membership and in the probability of occurence of the event, and (2) a diagnostic and a prognostic tools are derived from the model for early detection of the clinical event using any available information about the longitudinal markers.

Data Interpretation, Statistical↗

PubMed2001

Balanced neurons: analysis of leaky integrate-and-fire neurons with reversal potentials.

A new technique is presented for analyzing leaky integrate-and-fire neurons that incorporates reversal potentials, which impose a biologically realistic lower bound to the membrane potential. The time distribution of the synaptic inputs is modeled as a Poisson process. The analysis is carried out in the Gaussian approximation, which comparison with numerical simulations confirms is most accurate in the limit of a large number of inputs. The hypothesis that the observed variability in the spike times of cortical neurons is caused by a balance of excitatory and inhibitory synaptic inputs is supported by the results for the coefficient of variation of the interspike intervals. Its value decreases with both increasing numbers and amplitude of inputs, and is consistently lower than 1.0 over a wide range of realistic parameter values. The dependence of the output spike rate upon the rate, number, and amplitude of the synaptic inputs, as well as upon the value of the inhibitory reversal potential, is given.

Action Potentials↗

PubMed1992

Heterogeneous distributions and dispersive photodissociation rates of benzo[a]pyrene diol-epoxide enantiomer-DNA and -poly(dG-dC).poly(dG-dC) adducts.

Two types of heterogeneity of adducts are illustrated and discussed utilizing non-line narrowed (S2----S0 laser excitation) and line-narrowed (excitation into the (0,0) origin band) fluorescence spectra at low temperatures. The first type (type A) is due to structurally distinct and/or energetically inequivalent conformers. The second one (type B) is provided by an inhomogeneous environment of DNA and polynucleotides. In light of the above, the non-exponential photodissociation kinetics of the (+/-)-anti-BPDE-DNA and -polynucleotide adducts have been reanalyzed in terms of a dispersive first order chemical reaction, where the inhomogeneous effects are explicitly included. It is demonstrated that the DNA structure shows considerable inhomogeneous broadening, and that type B heterogeneity is responsible for the dispersive photodissociation process. The latter is accounted for by a Gaussian distribution of activation energies, with the center of the distribution at approximately 600 meV and the full width at half-maximum equal to approximately 50 meV (approximately 2 kT). Photolabile (+/-)-anti-BPDE-DNA and -polynucleotide adducts are identified as quasi-intercalated (site I) (+)- and (-)-cis-BPDE. The calculated concentrations of cis-BPDE adducts in DNA and polynucleotides from the kinetic data are in very good agreement with the cis-BPDE adduct concentrations obtained from the spectral and/or chemical analysis. The average photodissociation rate and the photodissociation quantum yield of cis- and trans-BPDE adducts are also estimated.

7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide↗

PubMed2004

Interresponse times and the structure of choice.

This paper presents some analyses of available data on interresponse-time emission on concurrent variable-interval schedules arranged either continuously or as discrete components, and in which either reinforcer rates or magnitudes were varied. Ratios of frequencies of interresponse times in a series of temporal bins varied in their sensitivity to reinforcement: Sensitivity values were least for interresponse times around 0.2-0.4s, were higher in the region 0-0.2s, and were highest at values greater than 0.4s. Relative frequencies of interresponse times were greatest around 0.2-1.6s. As a result, time allocation to alternatives were mainly determined by IRTs between 0.8 and 6.4s, and least by IRTs less than 0.8s. If inter-bout times reflect time allocation to unmeasured responses, then time spent emitting unmeasured behavior may be the main constituent of time allocation on concurrent schedules. An analysis of log survivor plots supported this suggestion, and further suggested that a full understanding of time allocation in choice requires accepting that unmeasured responses do not result from a unitary process, but from many disparate contributing processes. These other behaviors can be revealed through Gaussian log-normal analyses of interresponse-time distributions.

Animals↗

PubMed2002

Anisotropic NMR interaction tensors in the decamethylaluminocenium cation.

Solid-state NMR experiments, analytical and numerical simulations of solid NMR powder patterns, ab initio self-consistent field and hybrid density functional theory calculations, and single-crystal X-ray diffraction are used to characterize the molecular structure and anisotropic NMR interaction tensors in the bis(pentamethylcyclopentadienyl)aluminum cation, [Cp(2)Al](+). This highly symmetric main group metallocene has a structure analogous to that of ferrocene and the cobaltocenium cation. The single-crystal X-ray diffraction structure is reported for [Cp(2)Al][AlCl(4)]. Solid-state (27)Al[(1)H] magic-angle spinning and static NMR experiments are used to study the aluminum chemical shielding and electric field gradient tensors, revealing axial symmetry in both cases with a large chemical shielding span of Omega = 83(3) ppm and a small nuclear quadrupole coupling constant, C(Q)((27)Al) = 0.86(10) MHz. Carbon-13 CPMAS NMR experiments in combination with ab initio calculations and simulations of the effects of chemical exchange on (13)C static powder patterns reveal dynamic rotation of rings and suggest a low internal rotational barrier for this process. Theoretical computations of interaction tensors using the Gaussian 98 and Amsterdam Density Functional software packages are in good agreement with experiment and lend insight into the molecular origin of these NMR interactions. Orientations of the NMR tensors determined from theory, the large chemical shielding span, and the very small value of C(Q)((27)Al) can all be rationalized in terms of the high molecular symmetry.

Aluminum↗

PubMed1991

Evaluation of likelihood ratios for complex genetic models.

Although methods for computing likelihoods for simple genetic models on large and complex pedigrees have been known for some time, and although methods for evaluating likelihoods for complex genetic models on small pedigrees have likewise been well known, likelihood evaluation for complex models given data on extended pedigrees has remained an intractable problem. The Gibbs sampler provides a method of Monte Carlo evaluation of likelihood ratios for complex models on extended and/or complex pedigrees. With increasing computer speeds, this approach provides a tractable and efficient approach to many such likelihood evaluation problems in linkage and segregation analysis. In this paper, however, the authors restrict attention to two basic building-blocks of the overall process. The first is the sequential computation of Gaussian likelihoods for multiple random-effects models on extended pedigrees. The second is the use of this in the Monte Carlo evaluation of likelihoods for the classical mixed model of segregation analysis. The implementation of the Gibbs sampler on pedigrees that permits this Monte Carlo evaluation is detailed. An example is then presented, and finally, in the context of this same example, it is also shown how linkage analysis for a quantitative trait falls within this same framework.

Female↗

PubMed1978

[A new method for elimination of artifacts produced by collimator septum effect in gamma-camera images (author's transl)].

Collimator artifacts may be present within the images produced by collimators whose septal width approaches the inherent resolution of the gamma-camera system. As the inherent resolution of the gamma-camera is improved, collimator artifacts become more prominent. The purpose of this study is to eliminate collimator artifacts from gamma-camera images. To eliminate the septum effect produced by high-energy parallel-hole collimators with thick septa, the following method was used: X and Y signals from the detector are made to ride on the triangular waves changing periodically, and resultant position signals obtained by this processing are applied to the corresponding deflection circuits in the CRT display. The oscillation amplitude of processed position signals can be regulated by the frequency and amplitude of the triangular waves. Regulation of the oscillation amplitude of position signals, which would produce maximum reduction of collimator artifacts, was to approach the spatial frequency responses of the overall processed line spread functions obtained experimentally to those of the Gaussian functions with FWHM equal to the geometric resolution calculated from the equation given by Gerber and Miller. In images of a pancreas phantom containing 131I, collimator artifacts were clearly seen in the unprocessed case, but were eliminated in the processed case.

Models, Theoretical↗

PubMed2000

Measuring the complexity of time series: an application to neurophysiological signals.

Measures of signal complexity can be used to distinguish neurophysiological activation from noise in those neuroimaging techniques where we record variations of brain activity with time, e.g., fMRI, EEG, ERP. In this paper we explore a recently developed approach to calculate a quantitative measure of deterministic signal complexity and information content: The Renyi number. The Renyi number is by definition an entropy, i.e., a classically used measure of disorder in physical systems, and is calculated in this paper over the basis of the time frequency representation (TFRs) of the measured signals. When calculated in this form, the Renyi entropy (RE) indirectly characterizes the complexity of a signal by providing an approximate counting of the number of separated elementary atoms that compose the time series in the time frequency plane. In this sense, this measure conforms closely to our visual notion of complexity since low complexity values are obtained for signals formed by a small number of "components". The most remarkable properties of this measure are twofold: 1) It does not rely on assumptions about the time series such as stationarity or gaussianity and 2) No model of the neural process under study is required, e.g., no hemodynamic response model for fMRI. The method is illustrated in this paper using fMRI, intracranial ERPs and intracranial potentials estimated from scalp recorded ERPs through an inverse solution (ELECTRA). The main theoretical and practical drawbacks of this measure, especially its dependence of the selected TFR, are discussed. Also the capability of this approach to produce, with less restrictive hypothesis, results comparable to those obtained with more standard methods but is emphasized.

Algorithms↗

PubMedDate not supplied

[Helix-globule transitions of polypeptides selectively reacting with the interface].

An analytical theory of helix-coil transitions for polypeptides in a solution near a flat and homogeneous interface is given. The following cases were considered: a) only the helical parts are absorbtively active; b) only the coiled sections of the chain are active in adsorption. It has been shown that the binding of the polymer chain to the surface is a result of a phase transition of a second order, moreover in case a) the presence of a secondary structure abruptly increases the ability of the macromolecules to bind to the interface. This largely increases the stability of the helical structure of the chain and leads to a practically complete spiralization of the macromolecule. The profile of the conformational transitions was strictly asymmetrical which is typical for the phase transitions. In case b) the process of binding resembles the adsorbtion of the Gaussian coils. In this case the rate of spiralization of the chain decreases in the course of binding and the degradation of the secondary structure is significant even if the helical state in volume is stable. The profile of the transition remains qualitatively similar to the helix-coil transition in volume but is displaced to the region of larger equilibrium constants.

Models, Chemical↗