Automated SPE-RP-HPLC fractionation of biofluids combined to off-line NMR spectroscopy for biomarker identification in metabonomics

NMR-based metabonomics is a valuable and straightforward approach to measuring hundreds of metabolites in complex biofluids. However, metabolite identification is sometimes limited by overlapped signals in NMR spectra. We describe a new methodology using an automated hyphenation of solid phase extraction (SPE) with RP-HPLC combined to NMR spectroscopy, which allowed identification of 72 metabolites of various molecular classes in human urine. This methodology was also successfully applied to the fractionation of a cat urine sample to aid identification of aromatic compounds and felinine. The SPE-RP-HPLC method appears to be a reliable tool to support biomarker discovery in metabonomic studies.     

Hilbert-Huang transform for analysis of heart rate variability in cardiac health

This paper introduces a modified technique based on Hilbert-Huang transform (HHT) to improve the spectrum estimates of heart rate variability (HRV). In order to make the beat-to-beat (RR) interval be a function of time and produce an evenly sampled time series, we first adopt a preprocessing method to interpolate and resample the original RR interval. Then, the HHT, which is based on the empirical mode decomposition (EMD) approach to decompose the HRV signal into several monocomponent signals that become analytic signals by means of Hilbert transform, is proposed to extract the features of preprocessed time series and to characterize the dynamic behaviors of parasympathetic and sympathetic nervous system of heart. At last, the frequency behaviors of the Hilbert spectrum and Hilbert marginal spectrum (HMS) are studied to estimate the spectral traits of HRV signals. In this paper, two kinds of experiment data are used to compare our method with the conventional power spectral density (PSD) estimation. The analysis results of the simulated HRV series show that interpolation and resampling are basic requirements for HRV data processing, and HMS is superior to PSD estimation. On the other hand, in order to further prove the superiority of our approach, real HRV signals are collected from seven young health subjects under the condition that autonomic nervous system (ANS) is blocked by certain acute selective blocking drugs: atropine and metoprolol. The high-frequency power/total power ratio and low-frequency power/high-frequency power ratio indicate that compared with the Fourier spectrum based on principal dynamic mode, our method is more sensitive and effective to identify the low-frequency and high-frequency bands of HRV.     

Cross-population coupling of neural activity based on Gaussian process current source densities

Because local field potentials (LFPs) arise from multiple sources in different spatial locations, they do not easily reveal coordinated activity across neural populations on a trial-to-trial basis. As we show here, however, once disparate source signals are decoupled, their trial-to-trial fluctuations become more accessible, and cross-population correlations become more apparent. To decouple sources we introduce a general framework for estimation of current source densities (CSDs). In this framework, the set of LFPs result from noise being added to the transform of the CSD by a biophysical forward model, while the CSD is considered to be the sum of a zero-mean, stationary, spatiotemporal Gaussian process, having fast and slow components, and a mean function, which is the sum of multiple time-varying functions distributed across space, each varying across trials. We derived biophysical forward models relevant to the data we analyzed. In simulation studies this approach improved identification of source signals compared to existing CSD estimation methods. Using data recorded from primate auditory cortex, we analyzed trial-to-trial fluctuations in both steady-state and task-evoked signals. We found cortical layer-specific phase coupling between two probes and showed that the same analysis applied directly to LFPs did not recover these patterns. We also found task-evoked CSDs to be correlated across probes, at specific cortical depths. Using data from Neuropixels probes in mouse visual areas, we again found evidence for depth-specific phase coupling of primary visual cortex and lateromedial area based on the CSDs.     

Analysis of EEG signals during epileptic and alcoholic states using AR modeling techniques

Electroencephalogram (EEG) analysis remains problematic due to limited understanding of the signal origin, which leads to the difficulty of designing evaluation methods. In spite of these shortcomings, the EEG is a valuable tool in the evaluation of some neurological disorders as well as in the evaluation of overall cerebral activity. In most studies, which use quantitative EEG analysis, the properties of measured EEG are computed by applying power spectral density (PSD) estimation for selected representative EEG samples. The sample for which the PSD is calculated is assumed to be stationary. This work deals with a comparative study of the PSD obtained from normal, epileptic and alcoholic EEG signals. The power density spectra were calculated using fast Fourier transform (FFT) by Welch's method, auto regressive (AR) method by Yule–Walker and Burg's method. The results are tabulated for these different classes of EEG signals.     

The First Estimates of Marbled Cat Pardofelis marmorata Population Density from Bornean Primary and Selectively Logged Forest

The marbled cat Pardofelis marmorata is a poorly known wild cat that has a broad distribution across much of the Indomalayan ecorealm. This felid is thought to exist at low population densities throughout its range, yet no estimates of its abundance exist, hampering assessment of its conservation status. To investigate the distribution and abundance of marbled cats we conducted intensive, felid-focused camera trap surveys of eight forest areas and two oil palm plantations in Sabah, Malaysian Borneo. Study sites were broadly representative of the range of habitat types and the gradient of anthropogenic disturbance and fragmentation present in contemporary Sabah. We recorded marbled cats from all forest study areas apart from a small, relatively isolated forest patch, although photographic detection frequency varied greatly between areas. No marbled cats were recorded within the plantations, but a single individual was recorded walking along the forest/plantation boundary. We collected sufficient numbers of marbled cat photographic captures at three study areas to permit density estimation based on spatially explicit capture-recapture analyses. Estimates of population density from the primary, lowland Danum Valley Conservation Area and primary upland, Tawau Hills Park, were 19.57 (SD: 8.36) and 7.10 (SD: 1.90) individuals per 100 km², respectively, and the selectively logged, lowland Tabin Wildlife Reserve yielded an estimated density of 10.45 (SD: 3.38) individuals per 100 km². The low detection frequencies recorded in our other survey sites and from published studies elsewhere in its range, and the absence of previous density estimates for this felid suggest that our density estimates may be from the higher end of their abundance spectrum. We provide recommendations for future marbled cat survey approaches.     

Calculating luminous flux and lighting levels for domesticated mammals and birds

This paper considers whether photometric calculations using standard human spectral sensitivity data are satisfactory for applications with other species or whether it would be worthwhile to use bespoke spectral sensitivity functions for each species or group of species. Applications include the lighting of interior areas and the design of photometers. Published spectral sensitivity data for a number of domesticated animals (human, turkey, duck, chicken, cat, rat and mouse) were used to calculate lighting levels for each species and compared with those derived from standard CIE human photopic and scotopic functions. Calculations were made for spectral power distributions of daylight, incandescent light and 12 fluorescent sources commonly used to light interiors. The calculated lighting levels showed clear differences between species and the standard human. Assuming that the resulting effects on retinal illuminance determine the overall perception of the level of light, there may be applications where these differences are important. However, evidence is also presented that the magnitude of these inter-species effects are similar to, or smaller than, those arising from other optical, physiological and psychological factors, which are also likely to influence the resulting perception. It is also important to recognise that lighting-related parameters such as the good colour rendering of surfaces, the avoidance of glare from lamps and other factors that may be species related are sometimes of greater importance than the lighting levels. Our results suggest that a judicial choice of three spectral sensitivity functions would satisfy most circumstances. Firstly, where the overall sensitivity is maximal in the medium to long wavelengths, the standard CIE photopic function will suffice, chicken, turkey and duck fall in this category. Secondly, in a small number of cases where the sensitivity centres on the short to medium wavelengths, the CIE scotopic function should be used, e.g. for the scotopic cat, photopic rat and photopic mouse. Finally, where an animal is also sensitive to the UV region of the spectrum and there is a significant component of UV radiation, then an additional measure of the UV response should be included, as for the photopic rat and photopic mouse.     

System identification of photosensitiser uptake kinetics in photodynamic therapy

This study draws the interest of system identification to the experimental modelling of in vitro uptake kinetics of photosensitising agents (PS) into cancer cells. The proposed identification methodology must be usable and valid for every PS. Therefore, three PSs characterized by opposing chemical and biological properties have been selected: (1) PC: a second generation photosensitising agent conjugated via a spacer to a VEGF receptor-specific heptapeptide, (2) Ce6: Chlorin e6, and (3) TPP: TetraPhenylPorphyrin. Experiments have been carried out with two rates (2% and 9%) of foetal bovin serum in the culture medium and one cancer cell line U87 a human malignant glioma. Difficulties of such an application are triple: (i) lack of data, (ii) low signal-to-noise ratio and (iii) ‘poor’ stimulus signals. The proposed identification methodology deals with the design of experiments, the selection of a model structure, the estimation of the model parameters and the estimation of the parameter uncertainties. The photosensitiser uptake phenomenon is described by a first-order transfer function. Estimates of the time constant and the static gain provide quantitative information about the uptake rate and yield of the PS. The parameter uncertainty is described by confidence regions in parameters space. This representation is presented as an efficient way to discriminate the uptake characteristics of different photosensitisers. This representation also emphasizes the effects of some biological factors, such as the serum rate, on the uptake yield.     

Transmission of electric fields in cortical tissue: A model for the origin of the alpha rhythm

A mathematical model of the cortex is developed, in which a great many independently-firing sources of voltage pulses are assumed to be imbedded in a diffusive medium of indefinite extent. In such a medium, characterized by a conductivity and a capacitivity (capacitance per unit volume), electrical disturbances diffuse in a manner analogous to the conduction of heat in solids. Assuming random firing of the individual pulse sources (which simulate neurons) and invoking Campbell's Theorem, the power spectrum of the voltage appearing at any point within the medium can be calculated. As a consequence of the positive after-potential in the neural discharge (which is shown to be a physical necessity), the power spectrum is found to contain a single low-frequency peak. For reasonable parameter values, this peak appears at very near the classical alpha frequency of ten cycles per second. The related phenomena of evoked potentials, alpha blocking, and photic driving are also discussed in terms of the model.     

Seizure source localization using a hybrid second order blind identification and extended rival penalized competitive learning algorithm

Localization of seizure sources prior to neurosurgery is crucial. In this paper, a new method is proposed to localize the seizure sources from multi-channel electroencephalogram (EEG) signals. Blind source separation based on second order blind identification (SOBI) is primarily applied to estimate the brain source signals in each window of the EEG signals. A new clustering method based on rival penalized competitive learning (RPCL) is then developed to cluster the rows of the estimated unmixing matrices in all the windows. The algorithm also includes pre and post-processing stages. By multiplying each cluster center to the EEG signals, the brain signal sources are approximated. According to a complexity value measure, the main seizure source signal is separated from the others. This signal is projected back to the electrodes’ space and is subjected to the dipole source localization using a single dipole model. The simulation results verify the accuracy of the system. In addition, correct localization of the seizure source is consistent with the clinical tests derived using the simultaneous intracranial recordings.     

Advanced high-power pulsed light device to decontaminate food from pathogens: effects on Salmonella typhimurium viability in vitro

AIMS: The aim of this study was to construct an advanced high-power pulsed light device for decontamination of food matrix and to evaluate its antibacterial efficiency. Key parameters of constructed device-emitted light spectrum, pulse duration, pulse power density, frequency of pulses, dependence of emitted spectrum on input voltage, irradiation homogenicity, possible thermal effects as well as antimicrobial efficiency were evaluated. METHODS AND RESULTS: Antimicrobial efficiency of high-power pulsed light technique was demonstrated and evaluated by two independent methods - spread plate and Miles-Misra method. Viability of Salmonella typhimurium as function of a given light dose (number of pulses) and pulse frequency was examined. According to the data obtained, viability of Salmonella typhimurium reduced by 7 log order after 100 light pulses with power density 133 W cm(-2). In addition, data indicate, that the pulse frequency did not influence the outcome of pathogen inactivation in the region 1-5 Hz. Moreover, no hyperthermic effect was detected during irradiation even after 500 pulses on all shelves with different distance from light source and subsequently different pulse power density (0-252 W cm(-2)). CONCLUSION: Newly constructed high-power pulsed light technique is effective nonthermal tool for inactivation of Salmonella typhimurium even by 7 log order in vitro. SIGNIFICANCE AND IMPACT OF THE STUDY: Novel advanced high-power pulsed light device can be a useful tool for development of nonthermal food decontamination technologies.     

Estimation of the seed dispersal kernel from exact identification of source plants

The exact identification of individual seed sources through genetic analysis of seed tissue of maternal origin has recently brought the full analytical potential of parentage analysis to the study of seed dispersal. No specific statistical methodology has been described so far, however, for estimation of the dispersal kernel function from categorical maternity assignment. In this study, we introduce a maximum-likelihood procedure to estimate the seed dispersal kernel from exact identification of seed sources. Using numerical simulations, we show that the proposed method, unlike other approaches, is independent of seed fecundity variation, yielding accurate estimates of the shape and range of the seed dispersal kernel under varied sampling and dispersal conditions. We also demonstrate how an obvious estimator of the dispersal kernel, the maximum-likelihood fit of the observed distribution of dispersal distances to seed traps, can be strongly biased due to the spatial arrangement of seed traps relative to source plants. Finally, we illustrate the use of the proposed method with a previously published empirical example for the animal-dispersed tree species Prunus mahaleb.     

An interpretation of 1/f fluctuations in neuronal spike trains during dream sleep

The mesencephalic reticular formation (MRF) neurons are regarded as contributing to the activation of the cerebral cortex. We have investigated the statistical characteristics of the single neuronal activity in the MRF of cat during two activated states: paradoxical sleep (PS) and state in which the animal is watching birds (BW). 1/f-like spectra are observed for both PS and BW states, being more pronounced for PS state. For the interpretation of these findings, we have applied the clustering Poisson process, which not only gives rise to a 1/f spectrum but also suggests a generation mechanism. The MRF neuronal activities in PS and BW are closely fitted by the clustering Poisson process, both in terms of power spectral density and counting statistics. These results strongly suggest that the activities of MRF neurons in PS and BW can be interpreted as the superpositions of randomly occurring clusters which consist of various number of impulses.     

Effect of experimental methodology on estimation of density at sex initiation in cyclically parthenogenetic rotifers

Sexual reproduction is density-dependent in several cyclically parthenogenetic rotifer species and induced by a chemical signal produced by the rotifers. As population density increases, the chemical accumulates in the medium until reaching a threshold that triggers sex. The density threshold for sex initiation is of ecological and evolutionary importance due to the large impact that timing of sex has on fitness in cyclical parthenogenetic rotifers. Here we study the effects of experimental methodology in combination with intrinsic features of the biological system on the estimation of the density required to produce enough of this chemical to initiate sex (i.e., density threshold). We have developed a theoretical model describing the dynamics of both population density and the concentration of the chemical signal. Model analysis showed that the time at which sex is recorded in an experiment, the initial density (i.e., experimental volume) and the population growth rate can affect the estimation of density thresholds. Results from an experiment in which density at sex initiation was tested for 29 clones of Brachionus plicatilis at two culture volumes, revealed that density threshold is negatively dependent on the experimental volume. We conclude that in order to estimate density thresholds so that they are comparable across studies, experimental methodology should be standardized.     

Avian assemblage structure and domestic cat densities in urban environments

While there is intense debate regarding the impact of domestic cat populations on wildlife, its resolution is hindered by the lack of quite basic information. Domestic cats are generalist and obligate predators that receive supplementary food, and their population density reflects that of humans more than the density of their prey. In such a predator–prey system there is the potential for cat populations to have negative impacts on avian assemblages, which may be indicated by negative correlations between cat density and avian species richness and density. Here we report on the nature of such correlations across urban areas in Britain both for groups of species classified regarding their vulnerability to cat predation and individual species. Taking the availability of green space into account, we find negative relationships between cat densities and the number of bird species breeding in urban 1 km × 1 km squares. These relationships are particularly strong among groups of species that are vulnerable to cat predation. We find positive correlations between cat and avian densities; these have low explanatory power and shallow slopes among the species groups that are particularly vulnerable to cat predation. Evidence that the densities of individual species that are vulnerable to cat predation are negatively correlated with cat densities is equivocal, with at least half the species showing no marked pattern, and the remainder exhibiting contrasting patterns. Our results appear not to be confounded by the density of nest‐predating corvids (carrion crow, magpie, and jay), as the density of these species was not strongly negatively correlated with avian species richness or density. The general lack of marked negative correlations between cat and avian densities at our focal spatial scale may be a consequence of consistently high cat densities in our study areas (minimum density is 132 cats per square kilometre), and thus uniformly high impacts of cat populations on urban avian assemblages.     

The determination of the absolute configurations of chiral molecules using vibrational circular dichroism (VCD) spectroscopy

The vibrational circular dichroism (VCD) spectra of the two enantiomers of a chiral molecule are of equal magnitude and opposite sign: i.e. mirror-image enantiomers give mirror-image VCD spectra. In principle, the absolute configuration (AC) of a chiral molecule can therefore be determined from its VCD spectrum. In practice, the determination of the AC of a chiral molecule from its experimental VCD spectrum requires a methodology which reliably predicts the VCD spectra of its enantiomers. The only reliable methodology developed to date uses the Stephens quantum-mechanical theory of the rotational strengths of fundamental vibrational transitions, developed in the early 1980s, implemented using ab initio density functional theory in the GAUSSIAN program in the mid 1990s. This methodology has by now been widely used in determining ACs from experimental VCD spectra. In this article we discuss the protocol for determining the ACs of chiral molecules with optimum reliability and its implementation for a variety of molecules, including the D3 symmetry perhydrotriphenylene, a thiazino-oxadiazolone recently shown to be a highly active calcium entry channel blocker, the alkaloid natural products schizozygine, iso-schizogaline, and iso-schizogamine, and the iridoid natural products plumericin, iso-plumericin, and prismatomerin. The power of VCD spectroscopy in determining ACs, even for large organic molecules and for substantially conformationally-flexible organic molecules is clearly documented.     

Time-dependent power spectral density estimation of surface electromyography during isometric muscle contraction: Methods and comparisons

This paper studies the time-dependent power spectral density (PSD) estimation of nonstationary surface electromyography (SEMG) signals and its application to fatigue analysis during isometric muscle contraction. The conventional time-dependent PSD estimation methods exhibit large variabilities in estimating the instantaneous SEMG parameters so that they often fail to identify the changing patterns of short-period SEMG signals and gauge the extent of fatigue in specific muscle groups. To address this problem, a time-varying autoregressive (TVAR) model is proposed in this paper to describe the SEMG signal, and then the recursive least-squares (RLS) and basis function expansion (BFE) methods are used to estimate the model coefficients and the time-dependent PSD. The instantaneous parameters extracted from the PSD estimation are evaluated and compared in terms of reliability, accuracy, and complexity. Experimental results on synthesized and real SEMG data show that the proposed TVAR-model-based PSD estimators can achieve more stable and precise instantaneous parameter estimation than conventional methods.     

A transformation‐based approach to Gaussian mixture density estimation for bounded data

Finite mixture of Gaussian distributions provide a flexible semiparametric methodology for density estimation when the continuous variables under investigation have no boundaries. However, in practical applications, variables may be partially bounded (e.g., taking nonnegative values) or completely bounded (e.g., taking values in the unit interval). In this case, the standard Gaussian finite mixture model assigns nonzero densities to any possible values, even to those outside the ranges where the variables are defined, hence resulting in potentially severe bias. In this paper, we propose a transformation‐based approach for Gaussian mixture modeling in case of bounded variables. The basic idea is to carry out density estimation not on the original data but on appropriately transformed data. Then, the density for the original data can be obtained by a change of variables. Both the transformation parameters and the parameters of the Gaussian mixture are jointly estimated by the expectation‐maximization (EM) algorithm. The methodology for partially and completely bounded data is illustrated using both simulated data and real data applications.     

Significance and assessment of autonomic indices in cardiovascular reactions.

The purpose of this review was to integrate recent evidence supporting the reliability of noninvasive measures of parasympathetic and sympathetic activity. Literature concerning spectral analysis of heart period (HP) variability is reviewed with special emphasis on works revealing neural mediation of high-frequency and mid-frequency components of HP power spectrum and suggesting their use as a tool to assess autonomic balance. Problems of derivations of autonomic indices based on impedance cardiography and HP variance analysis are discussed. Advantages of parametric time series (autoregressive-AR) models are described with the objective of providing an informed basis for choosing among methodological alternatives. Two original approaches developed in our laboratory are outlined, namely the algorithms for systolic time interval assessment based on impedance cardiogram as well as the AR method developed for heart period power spectral density estimation.