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PubMed2000

Formulation for electromagnetic scattering and propagation through grating stacks of metallic and dielectric cylinders for photonic crystal calculations. Part II. Properties and implementation.

A numerical implementation and generalized conservation properties of a formulation for calculating wave propagation through stacked gratings comprising metallic and dielectric cylinders are presented. The basic formulation of the method was given in a companion paper [J. Opt. Soc. Am. A. 17, 2165 (2000)]. Here, details of the numerical implementation of the method are discussed and are illustrated for the ensemble average of a strongly scattering structure with refractive index and radius disorder. Also presented are a comprehensive treatment of energy conservation and generalized phase relations, as well as reciprocity.

Journal Article↗
PubMed2026

Integrating machine learning and GWAS for variant prioritization in the INCIPE cohort highlights ABC transporter genes in chronic kidney disease.

INTRODUCTION: Chronic kidney disease (CKD) is a major public health challenge, affecting approximately 674 million people worldwide and representing one of the fastest-growing causes of mortality. Since CKD is frequently asymptomatic in its early stages, the identification of novel genetic biomarkers may improve early detection and risk stratification. Genome-Wide Association Studies (GWAS) have identified numerous genetic loci associated with CKD and related traits; however, their performance is often limited in small and imbalanced cohorts, where reduced statistical power increases both false-positive and false-negative findings. Machine learning (ML) approaches can complement conventional GWAS by prioritizing biologically relevant genetic signals from high-dimensional genomic data. METHODS: In this study, we implemented a nested ensemble (NCBC) model composed of an undersampler and a CatBoostClassifier (CBC) to prioritize candidate genetic variants associated with CKD in the INCIPE cohort. Prioritized variants were functionally annotated and evaluated through enrichment analyses, GTEx gene expression profiling, and protein-protein interaction network analyses. Genes identified by the CKDGen Consortium were analysed as an external reference set and used to validate the biological relevance of the prioritized results. RESULTS: The NCBC model outperformed conventional ML classifiers, achieving a ROC AUC score of 87.77%, compared to 50%-53% for the other evaluated models. Among the prioritized genes, 56.25% showed protein-protein interactions with genes previously reported by the CKDGen Consortium, whereas only 1.9% of randomly generated gene sets showed interactions. DISCUSSION: Our study demonstrates that the NCBC model improves the prioritization of biologically plausible candidate variants in a small and imbalanced CKD cohort. Functional analyses suggested ABC transporter-related genes, including ABCA13, ABCA4, and ABCC4 genes, as promising candidate for future validation, with ABCA4 showing substantial expression in kidney tissues. Overall, these findings support the integration of ML with GWAS to prioritize candidate genes and investigate the genetic architecture of complex diseases.

SNP prioritization↗
PubMed2006

RNA expression profiling at the single molecule level.

We developed a microarray platform for PCR amplification-independent expression profiling of minute samples. A novel scanning system combined with specialized biochips enables detection down to individual fluorescent oligonucleotide molecules specifically hybridized to their complementary sequence over the entire biochip surface of cm2 size. A detection limit of 1.3 fM target oligonucleotide concentration--corresponding to only 39,000 molecules in the sample solution--and a dynamic range of 4.7 orders of magnitude have been achieved. The applicability of the system to PCR amplification-independent gene-expression profiling of minute samples was demonstrated by complex hybridization of cDNA derived from the equivalent of only 10(4) cells, which matches results obtained in ensemble studies on large samples. By counting each hybridized molecule on the microarray, the method is insusceptible to gene-specific variations of the labeling, thereby representing a principle advance to conventional ensemble-based microarray analysis.

Cell Line↗
PubMed2002

Statistical mechanics of typical set decoding.

The performance of "typical set (pairs) decoding" for ensembles of Gallager's linear code is investigated using statistical physics. In this decoding method, errors occur, either when the information transmission is corrupted by atypical noise, or when multiple typical sequences satisfy the parity check equation as provided by the received corrupted codeword. We show that the average error rate for the second type of error over a given code ensemble can be accurately evaluated using the replica method, including the sensitivity to message length. Our approach generally improves the existing analysis known in the information theory community, which was recently reintroduced in IEEE Trans. Inf. Theory 45, 399 (1999), and is believed to be the most accurate to date.

Journal Article↗
PubMed1984

Electromyographic amplitude normalization methods: improving their sensitivity as diagnostic tools in gait analysis.

The effect of four amplitude normalization methods on intersubject variability of electromyographic (EMG) profiles in normal gait was examined. Bipolar silver/silver chloride surface electrodes were applied to the rectus femoris, vastus lateralis, biceps femoris, tibialis anterior, and soleus muscles of the right lower extremity, in 11 healthy subjects. The myoelectric signals were telemetered via an FM multichannel biotelemetry system, full-wave rectified and low-pass filtered, then A/D converted together with the footswitch signal. Within-subject ensemble-average patterns were generated from the linear envelope EMG of at least six strides for each subject. Each subject's ensemble average was then normalized to the following: (a) the average EMG over three 50% isometric maximum voluntary contractions (MVC), (b) the EMG per unit isometric moment of force, (c) the peak of the subject ensemble average, (d) the mean of the subject ensemble average. Intersubject variability was quantified for each of the normalization methods by the coefficient of variation (CV). The normalization to either the peak ensemble or the mean ensemble drastically reduced intersubject variability, by 12%-73%. In contrast, normalization to the average EMG during 50% MVC or to the EMG per unit moment increased intersubject variability. It was concluded that the reduction of intersubject variability by appropriate amplitude normalization is possible, thereby increasing the sensitivity of surface EMG as a diagnostic tool in gait analysis.

Adolescent↗
PubMed1997

Analysis of phase-locking is informative for studying event-related EEG activity.

A new method is presented for quantitative evaluation of single-sweep phase and amplitude electro-encephalogram (EEG) characteristics that is a more informative approach in comparison with conventional signal averaging. In the averaged potential, phase-locking and amplitude effects of the EEG response cannot be separated. To overcome this problem, single-trial EEG sweeps are decomposed into separate presentations of their phase relationships and amplitude characteristics. The stability of the phase-coupling to stimulus is then evaluated independently by analyzing the single-sweep phase presentations. The method has the following advantages: information about stability of the phase-locking can be used to assess event-related oscillatory activity; the method permits evaluation of the timing of event-related phase-locking; and a global assessment and comparison of the phase-locking of ensembles of single sweeps elicited in different processing conditions is possible. The method was employed to study auditory alpha and theta responses in young and middle-aged adults. The results showed that whereas amplitudes of frequency responses tended to decrease, the phase-locking increased significantly with age. The synchronization with stimulus (phase-locking) was the only parameter reliably to differentiate the brain responses of the two age groups, as well as to reveal specific age-related changes in frontal evoked alpha activity. Thus, the present approach can be used to evaluate dynamic brain processes more precisely.

Adult↗
PubMed2004

PSTH-based classification of sensory stimuli using ensembles of single neurons.

The problem of understanding how ensembles of neurons code for somatosensory information has been defined as a classification problem: given the response of a population of neurons to a set of stimuli, which stimulus generated the response on a single-trial basis? Multivariate statistical techniques such as linear discriminant analysis (LDA) and artificial neural networks (ANNs), and different types of preprocessing stages, such as principal and independent component analysis, have been used to solve this classification problem, with surprisingly small performance differences. Therefore, the goal of this project was to design a new method to maximize computational efficiency rather than classification performance. We developed a peri-stimulus time histogram (PSTH)-based method, which consists of creating a set of templates based on the average neural responses to stimuli and classifying each single trial by assigning it to the stimulus with the 'closest' template in the Euclidean distance sense. The PSTH-based method is computationally more efficient than methods as simple as linear discriminant analysis, performs significantly better than discriminant analyses (linear, quadratic or Mahalanobis) when small binsizes are used (1 ms) and as well as LDA with any other binsize, is optimal among other minimum-distance classifiers and can be optimally applied on raw neural data without a previous stage of dimension reduction. We conclude that the PSTH-based method is an efficient alternative to more sophisticated methods such as LDA and ANNs to study how ensemble of neurons code for discrete sensory stimuli, especially when datasets with many variables are used and when the time resolution of the neural code is one of the factors of interest.

Action Potentials↗
PubMed2004

Dynamics of first-order phase transitions in multicomponent systems: a new theoretical approach.

In the theoretical description of nucleation-growth processes, currently Gibbs's classical thermodynamic theory of heterogeneous systems is predominantly employed for the description of the properties of the clusters. However, Gibbs's approach does not make it possible to describe, in general, the properties of critical clusters (determining the rate of nucleation) in a sufficiently correct way. Moreover, Gibbs's approach is restricted by its applicability to thermodynamic equilibrium states exclusively. For this reason, it does not give a theoretically founded prescription for a determination of the possible states of clusters of sub- and supercritical sizes in dependence on supersaturation and size of the clusters. In order to overcome these shortcomings, in recent years a generalization of Gibbs's classical approach has been developed and employed for the description of nucleation processes. This generalization of Gibbs' classical method leads, for a variety of different applications, to dependencies of the work of critical cluster formation on supersaturation, which are qualitatively and widely even quantitatively in agreement with density-functional computations. The theoretical methods and results are summarized in the first part of the present paper. They are then extended for the first time to a description of processes of growth of single clusters and ensembles of clusters. In order to fulfill this task, a new method for determination of the parameters of sub- and supercritical clusters is developed. It turns out as the result of the analysis that a variety of thermodynamic and kinetic parameters, determining cluster growth, become dependent on cluster size as well. The results are illustrated for a model system (segregation in regular solutions) and applied to the interpretation of experimental results on segregation processes in solutions and crystallization processes in glass-forming melts. It is shown that the newly developed approach resolves a variety of problems in the interpretation of experimental data on the kinetics of phase formation processes which could not be given a satisfactory explanation so far.

Journal Article↗
PubMed2001

Quantification of ATOFMS data by multivariate methods.

Aerosol time-of-flight mass spectrometry (ATOFMS) is capable of measuring the sizes and chemical compositions of individual polydisperse aerosol particles in real time. A qualitative estimate of the particle composition is acquired in the form of a mass spectrum that must be subsequently interpreted in order to draw conclusions regarding atmospheric relevance. The actual problem involves developing a calibration that allows the mass spectral data to be transformed into estimates of the composition of the atmospheric aerosol. A properly calibrated ATOFMS system should be able to quantitatively determine atmospheric concentrations of various species. Ideally, it would be able to accomplish this more rapidly, accurately, with higher size and time resolution, and at a far lower marginal cost than the manual sampling methods that are currently employed. Attempts have already been made at using ATOFMS and similar techniques to extract the bulk chemical species concentration present in an ensemble of particles. This study represents the use of a multivariate calibration method, two-dimensional partial least-squares analysis, for calibrating single-particle mass spectral data. The method presented here is far less labor-intensive than the univariate methods attempted to date and allows for less observer bias. Because of the labor savings, this is also the most comprehensive calibration performed to date, resulting in the quantification of 44 different chemical species.

Aerosols↗
PubMed1999

Heat stress and protective clothing: an emerging approach from the United States.

There is little doubt that heat stress affects many workers adversely and that protective clothing generally adds to the burden. The ACGIH threshold limit value for heat stress is the guiding document for evaluation of heat stress in the United States. Adjustment factors have been used to reflect the change in heat stress imposed by different clothing ensembles. While the first proposed factors started with limited experimental data and professional judgment, heat balance methods in the laboratory have yielded better estimates of adjustment factors and for a wider selection of ensembles. These same experiments have provided the starting point to accounting for nonporous clothing in heat balance evaluation schemes such as required sweat rate. Proposed changes to the ACGIH TLV have been mentioned and a framework for thinking about controls presented.

Body Temperature Regulation↗
PubMed1983

Towards fully objective evoked response audiometry.

The amplitude spectra of the auditory brainstem potentials evoked by free-field stimuli revealed significant differences from the corresponding spectra of pre-stimulus records. This was most marked for low order harmonics and in response to high intensity stimuli. In general, however, the shape of the amplitude spectrum for pre-stimulus and post-stimulus epochs was similar and the magnitude of the differences between corresponding harmonics became progressively smaller as stimulus intensity was reduced. Given that the spectrum of each coherent grand average is a function of the amplitude and phase spectra of the response ensemble, these were separately examined. Ensemble mean amplitude of individual harmonics diminished with stimulus intensity while their phases became progressively less aggregated. Phase standard deviation, used as a parameter of this aggregation, was found to change more systemically with stimulus intensity than ensemble mean amplitude. Phase standard deviation values for threshold responses were generally significantly smaller than corresponding harmonics obtained from sub-threshold responses. By contrast the amplitude differences between populations of threshold and sub-threshold responses were generally non-significant. These findings suggested that fully objective methods of threshold determination might more successfully be based on ensemble phase measures rather than amplitude measures.

Animals↗
PubMed2003

Numerical studies of the transport behavior of a passive solute in a two-dimensional incompressible random flow field.

We study the transport behavior of a passive scalar in a two-dimensional (2D) time-independent Gaussian random velocity field by efficient and highly accurate numerical simulations. The model under consideration has been used in order to gain basic understanding of transport processes in incompressible flow through heterogeneous porous media. The velocity field is derived from the linearized solution of the Darcy equation with a Gauss-distributed log-hydraulic conductivity. The transport of a passive scalar is studied by a high precision random-walk method, which allows for a systematic nonperturbative study of the ensemble and effective dispersion coefficients. The conclusive numerical results validate the range of applicability of the perturbation theory and the consistency of nonperturbative approaches to the transport problem in a random medium. Furthermore, we observe closed streamlines in incompressible 2D Gaussian random fields, which restricts the direct applicability of the simulation method for transport in heterogeneous porous media, and questions the results of similar studies that do not observe this phenomenon.

Journal Article↗
PubMed2004

Adsorption of ethylene on graphitized thermal carbon black and in slit pores: a computer simulation study.

In this paper, we studied vapor-liquid equilibria (VLE) and adsorption of ethylene on graphitized thermal carbon black and in slit pores whose walls are composed of graphene layers. Simple models of a one-center Lennard-Jones (LJ) potential and a two-center united atom (UA)-LJ potential are investigated to study the impact of the choice of potential models in the description of VLE and adsorption behavior. Here, we used a Monte Carlo simulation method with grand canonical Monte Carlo (GCMC) and Gibbs ensemble Monte Carlo ensembles. The one-center potential model cannot describe adequately the VLE over the practical range of temperature from the triple point to the critical point. On the other hand, the two-center potential model (Wick et al. J. Phys. Chem. B 2000, 104, 8008-8016) performs well in the description of VLE (saturated vapor and liquid densities and vapor pressure) over the wide range of temperature. This UA-LJ model is then used in the study of adsorption of ethylene on graphitized thermal carbon black and in slit pores. Agreement between the GCMC simulation results and the experimental data on graphitized thermal carbon black for moderate temperatures is excellent, demonstrating that the potential of the GCMC method and the proper choice of potential model are essential to investigate adsorption. For slit pores of various sizes, we have found that the behavior of ethylene exhibits a number of features that are not manifested in the study of spherical LJ particles. In particular, the singlet density distribution versus distance across the pore and the angle between the molecular axis and the z direction provide rich information about the way molecules arrange themselves when the pore width is varied. Such an arrangement has been found to be very sensitive to the pore width.

Journal Article↗
PubMed2000

Structural thermodynamics of a random coil protein in guanidine hydrochloride.

An important problem in protein folding is to understand the relationship between the structure of a denatured ensemble and its thermodynamics. Using 0 - 6M GdnHCl at fixed pH, we evaluated dimensional changes of an extensively denatured ensemble along with a thermodynamic parameter (Deltaupsilon) that monitors the proton inventory of the ensemble. Reduced and carboxyamidated ribonuclease A (RCAM) is a member of a class of disulfide-free RNase A molecules believed to be random coils (extensively denatured) in aqueous solution. Because GdnHCl interacts more favorably with the protein than water does, this denaturant is observed to increase the Stokes radius of the random coil, with the greatest Stokes radius change occurring in the 0 - 1.5M GdnHCl range. Measurement of the degree of protonation (proton inventory) of the ensemble as a function of GdnHCl at the fixed pH shows that the thermodynamic character of the ensemble also changes markedly in the 0 - 1.5M GdnHCl range, but with little or no change beyond 1.5M GdnHCl. To obtain denaturant-independent DeltaG degrees (N-D) values, the linear extrapolation method (LEM) requires the thermodynamic character of the native and denatured ensembles to be invariant in the transition zone. The results reported here indicate that proteins with a transition midpoint in the 0 - 1.5M GdnHCl range will not give denaturant-concentration independent DeltaG degrees (N-D) values. Such LEM-derived DeltaG degrees (N-D) quantities are a property of the protein and the denaturant, a condition that considerably limits their value in understanding structural energetics.

Guanidine↗
PubMed2002

Nonnegative color spectrum analysis filters from principal component analysis characteristic spectra.

Nonnegative color analysis filters are obtained by using an invertible linear transformation of characteristic spectra, which are orthogonal vectors from a principal component analysis (PCA) of a representative ensemble of color spectra. These filters maintain the optimal compression properties of the PCA scheme. Linearly constrained nonlinear programming is used to find a transformation that minimizes the noise sensitivity of the filter set. The method is illustrated by computing analysis and synthesis filters for an ensemble of measured Munsell color spectra.

Journal Article↗
PubMed2002

Nonequilibrium statistical mechanics of mixed quantum classical ensembles: application to noncontact atomic force microscopy.

Using the nonequilibrium statistical operator method, we suggest a new general method of treating dynamics of a combined system consisting of interacting classical and quantum parts. The method is illustrated on the tip dynamics in the noncontact atomic force microscopy (NC-AFM) where a macroscopic tip interacts with a quantum microscopic system (the surface and the nanotip). The derived general equation of motion for the tip and the Fokker-Planck equation, applicable even at low temperatures, contain memory effects and a friction term which should (at least partially) be responsible for the observed energy dissipation in NC-AFM experiments.

Journal Article↗
PubMed2001

The pair-functional method. III. The pairing forces.

The theory of the pair-functional ensemble is developed to provide estimates of the pairing forces from experimental X-ray intensities. The statistical mechanics of the grand ensemble leads to a diagram expansion for the forces, in terms of the direct correlation function of the fluid ensemble combined with a series of small higher-order corrections. A simpler treatment, based on a biased Gaussian probability distribution, gives approximate formulae, valid for reflections of any type in all space groups. The role of symmetry is analysed. The entropy of an asymmetrical ensemble can always be increased by averaging it over equivalent positions of the atoms in the true space group, with the result that the atoms naturally tend to adopt the highest symmetry compatible with the data. In a cell with different types of atom, the atoms experience a single force function but they interact with a strength proportional to the products of their scattering factors. Numerical estimates are given for typical cases.

Journal Article↗
PubMed2001

Feature analysis of natural sounds in the songbird auditory forebrain.

Although understanding the processing of natural sounds is an important goal in auditory neuroscience, relatively little is known about the neural coding of these sounds. Recently we demonstrated that the spectral temporal receptive field (STRF), a description of the stimulus-response function of auditory neurons, could be derived from responses to arbitrary ensembles of complex sounds including vocalizations. In this study, we use this method to investigate the auditory processing of natural sounds in the birdsong system. We obtain neural responses from several regions of the songbird auditory forebrain to a large ensemble of bird songs and use these data to calculate the STRFs, which are the best linear model of the spectral-temporal features of sound to which auditory neurons respond. We find that these neurons respond to a wide variety of features in songs ranging from simple tonal components to more complex spectral-temporal structures such as frequency sweeps and multi-peaked frequency stacks. We quantify spectral and temporal characteristics of these features by extracting several parameters from the STRFs. Moreover, we assess the linearity versus nonlinearity of encoding by quantifying the quality of the predictions of the neural responses to songs obtained using the STRFs. Our results reveal successively complex functional stages of song analysis by neurons in the auditory forebrain. When we map the properties of auditory forebrain neurons, as characterized by the STRF parameters, onto conventional anatomical subdivisions of the auditory forebrain, we find that although some properties are shared across different subregions, the distribution of several parameters is suggestive of hierarchical processing.

Animals↗