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PubMed2006

Phylogenetic mapping of recombination hotspots in human immunodeficiency virus via spatially smoothed change-point processes.

We present a Bayesian framework for inferring spatial preferences of recombination from multiple putative recombinant nucleotide sequences. Phylogenetic recombination detection has been an active area of research for the last 15 years. However, only recently attempts to summarize information from several instances of recombination have been made. We propose a hierarchical model that allows for simultaneous inference of recombination breakpoint locations and spatial variation in recombination frequency. The dual multiple change-point model for phylogenetic recombination detection resides at the lowest level of our hierarchy under the umbrella of a common prior on breakpoint locations. The hierarchical prior allows for information about spatial preferences of recombination to be shared among individual data sets. To overcome the sparseness of breakpoint data, dictated by the modest number of available recombinant sequences, we a priori impose a biologically relevant correlation structure on recombination location log odds via a Gaussian Markov random field hyperprior. To examine the capabilities of our model to recover spatial variation in recombination frequency, we simulate recombination from a predefined distribution of breakpoint locations. We then proceed with the analysis of 42 human immunodeficiency virus (HIV) intersubtype gag recombinants and identify a putative recombination hotspot.

Animals↗

PubMed1989

In vivo ultrasound backscattering estimation for tumour diagnosis: an animal study.

In this study the efficacy of a quantitative analysis of backscattered ultrasound for the differential diagnosis of intraocular tumours is tested. The data acquisition was performed with an on-line acquisition and processing system for in vivo work. The backscattering spectra were corrected for the beam effects (diffraction and focussing). The measurements were taken from an animal model (rabbit) in which a Greene's amelanotic melanoma was implanted in the anterior chamber of the eye. The special histologic arrangement of this tumour makes it optimally suited to an assessment of the correlation between histology and backscattering cross section. Various backscattering models were considered theoretically and the choice for a practical testing was motivated on the properties of the observed backscattering spectra. We conclude that the backscattering model based on an "inhomogeneous continuum" with a cylindrical Gaussian autocorrelation function fits the data optimally. The relatively low correlation of the backscattering cross-sections to histology cannot yet be fully explained. The range of acoustic scatterer sizes, however, corresponds quite well to the dimension of observed and quantified histologic structures.

Animals↗

PubMed1996

A model of ultrasound backscatter for the assessment of myocardial tissue structure and architecture.

A statistical parametric model of returning echoes from myocardium is theorized in order to investigate the relationship between normal myocardium structure and spectral signatures with the use of ultrasonic tissue characterization. It is hypothesized, that in a clinical setting the normal myofiber architecture in the left ventricular wall is structured as a matrix of cylinder scatterers whose orientation and spatial distribution vary according to two different statistical distribution laws: 1) a Gaussian law to approximate parametric angular myofiber variability at each site within the myocardial wall; 2) a gamma distribution law to describe parametric regularity in scatterer interdistance. In the model, the effect of the angle of insonification with respect to the alignment of myofibers on ultrasound backscatter was considered. The slope of the power spectral density (PSD) evaluated within the echocardiographic transducer bandwidth has been used as a ultrasonic tissue characterization parameter. The model has been tested by computer simulation and in vitro measurements on myocardial pig tissue specimens. The concordance between experimental and simulated results confirms that the model accounts for the process underlying the echo formation from normal myocardium. Moreover, it provides a simple method of simulation which can be easily implemented and used for the assessment of pathologic alterations.

Animals↗

PubMed1993

An asymmetric slice profile: spatial alteration of flow signal response in 3D time-of-flight NMR angiography.

We introduce an asymmetric slice profile technique, which alters the spatial response of the flow signal in 3D time-of-flight NMR angiography. By gradually increasing the flip angle from the inflow to the outflow portions of the slab, the inflow refreshment effect is distributed over a wide slab thickness. The asymmetric slice profile is simply produced by using a Gaussian RF excitation with an overlapping presaturation. The spatial distribution of steady flow signal in a phantom study demonstrated an essential agreement with a numerical simulation. 3D time-of-flight NMR angiography of volunteers' heads using this technique provided a smooth vascular depiction over a wide slab thickness.

Blood Vessels↗

PubMed2000

Wavelet domain nonlinear filtering for evoked potential signal enhancement.

A wavelet domain nonlinear filtering method for improving the signal-to-noise ratio (SNR) of the evoked potentials (EP) is proposed. The method modifies the selective filtering technique proposed for edge detection in images by Xu et al. for the case of signals which require a smooth transition at the edge points. It identifies the significant features of a noisy signal based on the correlation between the scales of its nonorthogonal subband decompositions. The signal transition information from interscale correlation coupled with the change in variance around the identified transition region is used to differentiate between noise and the signal. A nonlinear function such as a Gaussian smoothing function applied around the identified edge in the wavelet domain leads to smoothing in the signal space also. Numerical results obtained by applying the proposed nonlinear filtering method on middle latency responses of auditory evoked potentials show that the method is well suited for signal enhancement applications.

Evoked Potentials, Auditory↗

PubMed1987

The fractal dimension of a test signal: implications for system identification procedures.

The experimental identification of a non-linear biologic transducer is often approached via consideration of its response to a stochastic test ensemble, such as Gaussian white noise (Marmarelis and Marmarelis 1978). In this approach, the input-output relationship a deterministic transducer is described by an orthogonal series of functionals. Laboratory implementation of such procedures requires the use of a particular test signal drawn from the idealized stochastic ensemble; the statistics of the particular test signal necessarily deviate from the statistics of the ensemble. The notion of a fractal dimension (specifically the capacity dimension) is a means to characterize a complex time series. It characterizes one aspect of the difference between a specific example of a test signal and the test ensemble from which it is drawn: the fractal dimension of ideal Gaussian white noise is infinite, while the fractal dimension of a particular test signal is finite. This paper shows that the fractal dimension of a test signal is a key descriptor of its departure from ideality: the fractal dimension of the test signal bounds the number of terms that can reliably be identified in the orthogonal functional series of an unknown transducer.

Mathematics↗

PubMed2004

Evaluation of mixed effects in event-related fMRI studies: impact of first-level design and filtering.

With the introduction of event-related designs in fMRI, it has become crucial to optimize design efficiency and temporal filtering to detect activations at the 1st level with high sensitivity. We investigate the relevance of these issues for fMRI population studies, that is, 2nd-level analysis, for a set of event-related fMRI (er-fMRI) designs with different 1st-level efficiencies, adopting three distinct 1st-level filtering strategies as implemented in SPM99, SPM2, and FSL3.0. By theory, experiments, and simulations using physiological fMRI noise, we show that both design and filtering impact the outcome of the statistical analysis, not only at the 1st but also at the 2nd level. There are several reasons behind this finding. First, sensitivity is affected by both design and filtering, since the scan-to-scan variance, that is the fixed effect, is not negligible with respect to the between-subject variance, that is the random effect, in er-fMRI population studies. The impact of the fixed effects error on the sensitivity of the mixed effects analysis can be mitigated by an optimal choice of er-fMRI design and filtering. Moreover, the accuracy of the 1st- and 2nd-level parameter estimates also depend on design and filtering; especially, we show that inaccuracies caused by the presence of residual noise autocorrelations can be constrained by designs that have hemodynamic responses with a Gaussian distribution. In conclusion, designs with both good efficiency and decorrelating properties, for example, such as the geometric or Latin square probability distributions, combined with the "whitening" filters of SPM2 and FSL3.0, give the best result, both for 1st- and 2nd-level analysis of er-fMRI studies.

Adult↗

PubMed2003

Stochastic model for heart-rate fluctuations.

A normal human heart rate shows complex fluctuations in time, which is natural, because the heart rate is controlled by a large number of different feedback control loops. These unpredictable fluctuations have been shown to display fractal dynamics, long-term correlations, and 1/f noise. These characterizations are statistical and they have been widely studied and used, but much less is known about the detailed time evolution (dynamics) of the heart-rate control mechanism. Here we show that a simple one-dimensional Langevin-type stochastic difference equation can accurately model the heart-rate fluctuations in a time scale from minutes to hours. The model consists of a deterministic nonlinear part and a stochastic part typical to Gaussian noise, and both parts can be directly determined from the measured heart-rate data. Studies of 27 healthy subjects reveal that in most cases, the deterministic part has a form typically seen in bistable systems: there are two stable fixed points and one unstable one.

Cardiovascular System↗

PubMed2000

Study of the control strategy of the quadriceps muscles in anterior knee pain.

Anterior knee pain (AKP) is a common pathological condition, particularly among young people and athletes, associated to an abnormal motion of the patella during the bending of the knee and possibly dependent on a muscular or structural imbalance. A lack of synergy in the quadriceps muscles results in a dynamic misalignment of the patella, which in turn produces pain. AKP rehabilitative therapy consists of conservative treatment whose main objective is to strengthen the Vastus Medialis. The aim of this article is to study the quadriceps muscle control strategy in AKP patients during an isokinetic exercise. Analysis of the muscle activation strategy is important for an objective measurement of the knee functionality in that it helps to diagnose and monitor the rehabilitative treatment. Surface electromyography (EMG) from the three superficial muscles of the femoral quadriceps during a concentric isokinetic exercise has been analyzed along with the signals of knee joint position and torque. A group of 12 AKP patients has been compared with a group of 30 normal subjects. Analysis of the grand ensemble average of the EMG linear envelopes in AKP patients reveals significant modifications in Vastus Medialis activity compared to the other quadriceps muscles. In order to study the synergy of the muscles, temporal identifiers have been associated to the EMG linear envelopes. To this end, EMG linear envelope decomposition in Gaussian pulses turned out to be effective and the results highlight an appreciable delay in the activation of the Vastus Medialis in AKP patients. This muscular unbalance can explain the abnormal motion of the patella.

Adolescent↗

PubMed2004

Heidelberg retina tomograph measurements of the optic disc and parapapillary retina for detecting glaucoma analyzed by machine learning classifiers.

PURPOSE: To determine whether topographical measurements of the parapapillary region analyzed by machine learning classifiers can detect early to moderate glaucoma better than similarly processed measurements obtained within the disc margin and to improve methods for optimization of machine learning classifier feature selection. METHODS: One eye of each of 95 patients with early to moderate glaucomatous visual field damage and of each of 135 normal subjects older than 40 years participating in the longitudinal Diagnostic Innovations in Glaucoma Study (DIGS) were included. Heidelberg Retina Tomograph (HRT; Heidelberg Engineering, Dossenheim, Germany) mean height contour was measured in 36 equal sectors, both along the disc margin and in the parapapillary region (at a mean contour line radius of 1.7 mm). Each sector was evaluated individually and in combination with other sectors. Gaussian support vector machine (SVM) learning classifiers were used to interpret HRT sector measurements along the disc margin and in the parapapillary region, to differentiate between eyes with normal and glaucomatous visual fields and to compare the results with global and regional HRT parameter measurements. The area under the receiver operating characteristic (ROC) curve was used to measure diagnostic performance of the HRT parameters and to evaluate the cross-validation strategies and forward selection and backward elimination optimization techniques that were used to generate the reduced feature sets. RESULTS: The area under the ROC curve for mean height contour of the 36 sectors along the disc margin was larger than that for the mean height contour in the parapapillary region (0.97 and 0.85, respectively). Of the 36 individual sectors along the disc margin, those in the inferior region between 240 degrees and 300 degrees, had the largest area under the ROC curve (0.85-0.91). With SVM Gaussian techniques, the regional parameters showed the best ability to discriminate between normal eyes and eyes with glaucomatous visual field damage, followed by the global parameters, mean height contour measures along the disc margin, and mean height contour measures in the parapapillary region. The area under the ROC curve was 0.98, 0.94, 0.93, and 0.85, respectively. Cross-validation and optimization techniques demonstrated that good discrimination (99% of peak area under the ROC curve) can be obtained with a reduced number of HRT parameters. CONCLUSIONS: Mean height contour measurements along the disc margin discriminated between normal and glaucomatous eyes better than measurements obtained in the parapapillary region.

Area Under Curve↗

PubMed2006

Toward absolute density of states calculations for proteins.

The density of states (DOS), which gives the number of conformations with a particular energy E, is a prerequisite in computing most thermodynamic quantities and in elucidating important biological processes such as the mechanism of protein folding. However, current methods for computing DOS of large systems such as proteins generally yield only the ratios of microstate counts for different energies, which could yield absolute conformation counts if the total number of conformations in phase space is known, thus motivating this work. Here, the total number of energy minima of 50-mer polyalanine, whose size corresponds to naturally occurring small proteins, was estimated under an all-atom potential energy function based on the cumulative distribution function (CDF) of conformational differences to be approximately 10(38). This estimate can place any DOS function, such as the Gaussian DOS distribution in the random energy model, on an absolute scale. Comparing the absolute conformational counts from a Gaussian DOS function with those from the CDF derived from quenched molecular dynamics ensembles shows that the former are far greater than the latter, indicating far fewer low-energy minima actually exist. In addition to showing how CDF and relative DOS calculations can yield absolute DOS for a discrete system, we also show how they can yield absolute DOS for continuous variable systems to a specified atomic variance. In the context of protein folding, knowing this phase-space "volume" of conformations in a DOS function, as well as characteristic transition times, constrains the set of possible folding mechanisms.

Protein Conformation↗

PubMed2004

Direct patterning of self-assembled monolayers on gold using a laser beam.

The development of a methodology to manipulate surface properties of a self-assembled monolayer (SAM) of alkanethiol on a gold film using direct laser patterning is the objective of this paper. The present study demonstrates proof of the concept for the feasibility of laser patterning monolayers and outlines theoretical modeling of the process to predict the resulting feature size. This approach is unique in that it eliminates the need for photolithography, is noncontact, and can be extended to other systems such as SAMs on silicon wafers or potentially polymeric substrates. A homogeneous SAM made of 1-hexadecanethiol is formed on a 300-A sputtered film of gold (supported by a soda lime glass substrate). Localized regions are then desorbed by scanning the focal spot of a 488-nm continuous-wave argon ion laser beam under a nitrogen atmosphere. The desorption occurs as a result of a high substrate temperature produced by the moving laser beam with a Gaussian spatial profile at a constant speed of 200 microm/s. After completing the scans, the sample is dipped into a dilute solution of 16-mercaptohexadecanoic acid and a hydrophilic monolayer self-assembles along the previously irradiated regions. The resultant lines are viewed, and line widths are measured using both wetting with tridecane under a light microscope and scanning electron microscopy. Using the direct laser patterning method, we have produced straight line patterns with widths of 28-170 microm. A thermal model was constructed to predict the line width of the desorbed monolayer. The effect of the laser power, beam waist, and temperature dependence of the substrate conductivity on the theoretical predictions is considered. It is shown that the theoretical predictions are in good agreement with the experimental results, and, thus, the model can effectively be used to predict experimental results.

Adsorption↗

PubMed1983

Statistics of the maintained discharge of cat retinal ganglion cells.

Action potentials were recorded from single fibres in the optic tracts of anaesthetized cats. Continuous records were obtained at various levels of scotopic and mesopic retinal illumination. In some cases, the light intensity was modulated by a pseudorandom Gaussian white-noise signal. The maintained discharge of on-centre neurones increased while the maintained discharge of off-centre neurons decreased with increased illumination of the receptive field centre. For both cell types, the coefficient of variation declined with increased rate of discharge. There was minimal short-term dependency in the firing patterns, and it was unaffected by the level of retinal illumination. Virtually all of the structure revealed by the normalized autocovariance functions could be attributed to the shape of the interval distributions. The first few coefficients of the serial correlogram were slightly negative. The magnitude of this negativity was not related to illumination. Long-term dependency in the firing pattern was also quite small; the standard deviations of the mean rate in samples of about 1 sec duration were only slightly less than would be predicted from the interval distributions. This dependency tended to increase at higher retinal illuminations. Neural discharges elicited by Gaussian modulation of the light were strikingly different from those elicited by steady light. Modulation caused the first coefficient of the serial correlogram to become more positive, while the next several coefficients became more negative. A corresponding pattern could be seen in the normalized autocovariance functions, and in the differences between the normalized autocovariance and normalized autoconvolution. Long-term dependency also increased dramatically, such that the standard deviations of mean rate were about 60% of what would be expected given the interval distributions observed. These results place a number of constraints upon the ways in which intrinsic noise in the retina may enter the visual processing network. Two alternative models consistent with the data are presented.

Animals↗

PubMed2002

PTV margin determination in conformal SRT of intracranial lesions.

The planning target volume (PTV) includes the clinical target volume (CTV) to be irradiated and a margin to account for uncertainties in the treatment process. Uncertainties in miniature multileaf collimator (mMLC) leaf positioning, CT scanner spatial localization, CT-MRI image fusion spatial localization, and Gill-Thomas-Cosman (GTC) relocatable head frame repositioning were quantified for the purpose of determining a minimum PTV margin that still delivers a satisfactory CTV dose. The measured uncertainties were then incorporated into a simple Monte Carlo calculation for evaluation of various margin and fraction combinations. Satisfactory CTV dosimetric criteria were selected to be a minimum CTV dose of 95% of the PTV dose and at least 95% of the CTV receiving 100% of the PTV dose. The measured uncertainties were assumed to be Gaussian distributions. Systematic errors were added linearly and random errors were added in quadrature assuming no correlation to arrive at the total combined error. The Monte Carlo simulation written for this work examined the distribution of cumulative dose volume histograms for a large patient population using various margin and fraction combinations to determine the smallest margin required to meet the established criteria. The program examined 5 and 30 fraction treatments, since those are the only fractionation schemes currently used at our institution. The fractionation schemes were evaluated using no margin, a margin of just the systematic component of the total uncertainty, and a margin of the systematic component plus one standard deviation of the total uncertainty. It was concluded that (i) a margin of the systematic error plus one standard deviation of the total uncertainty is the smallest PTV margin necessary to achieve the established CTV dose criteria, and (ii) it is necessary to determine the uncertainties introduced by the specific equipment and procedures used at each institution since the uncertainties may vary among locations.

Brain Neoplasms↗

PubMed2001

Predictive modelling of NAPL injection tests in variable aperture spatially correlated fractures.

In preparation for a field experiment where a NAPL will be injected into a fractured sandstone aquifer, a 2D invasion percolation model of DNAPL migration in a single horizontal fracture with varying aperture has been developed. This simulation investigated the effect of spatially correlated fracture aperture fields on pressure-saturation relationships as a function of variable aperture mean, standard deviation, and spatial correlation statistics under hydrostatic conditions. Results from spatially correlated variable aperture fields can be significantly different from random fields. Longer ranges decreased entry pressures and higher standard deviations decreased nonwetting phase saturations. Mean aperture is the major control on displacement pressure, entry pressure and the form of the pressure-saturation curve. Simulation results using statistical parameters for a variable aperture natural sandstone fracture as described by Yeo et al. [International Journal of Rock Mechanics and Mining Sciences 35 (1998) 1051] closely resemble a Brooks-Corey pressure-saturation function, and exhibit a distinct entry pressure followed by a rapid increase in nonwetting phase saturation. Graphical estimates of entry pressure provide a good approximation of the critical aperture controlling the formation of a continuous nonwetting phase pathway in a variable aperture fracture. Consequently, we show that multiphase flow concepts developed for porous media can successfully be applied to variable aperture fractures. Entry pressure correlates well to the mean aperture in these simulations when using a Gaussian distribution of fracture aperture. Interpreted aperture distributions from NAPL injection experiments do not fit the true distribution well at low nonwetting phase saturations, but do at higher saturations above the entry pressure. Consequently, true, mechanical aperture variation within a fracture plane cannot be determined from NAPL injection experiments either in the field or laboratory.

Computer Simulation↗

PubMed2000

Selection and determination of beam weights based on genetic algorithms for conformal radiotherapy treatment planning.

A genetic algorithm has been used to optimize the selection of beam weights for external beam three-dimensional conformal radiotherapy treatment planning. A fitness function is defined, which includes a difference function to achieve a least-square fit to doses at preselected points in a planning target volume, and a penalty item to constrain the maximum allowable doses delivered to critical organs. Adjustment between the dose uniformity within the target volume and the dose constraint to the critical structures can be achieved by varying the beam weight variables in the fitness function. A floating-point encoding schema and several operators, like uniform crossover, arithmetical crossover, geometrical crossover, Gaussian mutation and uniform mutation, have been used to evolve the population. Three different cases were used to verify the correctness of the algorithm and quality assessment based on dose-volume histograms and three-dimensional dose distributions were given. The results indicate that the genetic algorithm presented here has considerable potential.

Adolescent↗

PubMed2000

SMEM algorithm for mixture models.

We present a split-and-merge expectation-maximization (SMEM) algorithm to overcome the local maxima problem in parameter estimation of finite mixture models. In the case of mixture models, local maxima often involve having too many components of a mixture model in one part of the space and too few in another, widely separated part of the space. To escape from such configurations, we repeatedly perform simultaneous split-and-merge operations using a new criterion for efficiently selecting the split-and-merge candidates. We apply the proposed algorithm to the training of gaussian mixtures and mixtures of factor analyzers using synthetic and real data and show the effectiveness of using the split-and-merge operations to improve the likelihood of both the training data and of held-out test data. We also show the practical usefulness of the proposed algorithm by applying it to image compression and pattern recognition problems.

Algorithms↗

PubMedDate not supplied

Transition state structure and energetics of the N(2)O + X (X = Cl,Br) reactions.

The structural and vibrational properties of the transition state of the N(2)O + X (X = Cl,Br) reactions have been characterized by ab initio methods using density functional theory. We have employed Becke's hybrid functional (B3LYP), and transition state optimizations were performed with 6-31G(d), 6-311G(2d,2p), 6-311+G(3d,2p), and 6-311+G(3df,2p) basis sets. For the chlorine atom reaction the coupled-cluster method (CCSD(T)) with 6-31G(d) basis set was also used. All calculations resulted in transition state structures with a planar cis arrangement of atoms for both reactions. The geometrical parameters of transition states at B3LYP are very similar, and the reaction coordinates involve mainly the breaking of the N-O bond. At CCSD(T)/6-31G(d) level a contribution of the O-Cl forming bond is also observed in the reaction coordinate. In addition, several highly accurate ab initio composite methods of Gaussian-n (G1, G2, G3), their variations (G2(MP2), G3//B3LYP), and complete basis set (CBS-Q, CBS-Q//B3LYP) series of models were applied to compute reaction energetics. All model chemistries predict exothermic reactions. The G3 and G2 methods result in the smallest deviations from experiment, 1.8 and 0 kcal mol(-1), for the enthalpies of reaction for N(2)O reaction with chlorine and bromine, respectively. The G3//B3LYP and G1 methods perform best among the composite methods in predicting energies of the transition state, with a deviation of 1.9 and 3.0 kcal mol(-1), respectively, in the activation energies for the above processes. However, the B3LYP/6-311+G(3df,2p) method gives smaller deviations of 0.4 and -1.0 kcal mol(-1), respectively. The performance of the methodologies applied in predicting transition state energies was analyzed.

Journal Article↗