Application of modern tests for stationarity to single-trial MEG data

Stationarity is a crucial yet rarely questioned assumption in the analysis of time series of magneto- (MEG) or electroencephalography (EEG). One key drawback of the commonly used tests for stationarity of encephalographic time series is the fact that conclusions on stationarity are only indirectly inferred either from the Gaussianity (e.g. the Shapiro-Wilk test or Kolmogorov-Smirnov test) or the randomness of the time series and the absence of trend using very simple time-series models (e.g. the sign and trend tests by Bendat and Piersol). We present a novel approach to the analysis of the stationarity of MEG and EEG time series by applying modern statistical methods which were specifically developed in econometrics to verify the hypothesis that a time series is stationary. We report our findings of the application of three different tests of stationarity--the Kwiatkowski-Phillips-Schmidt-Schin (KPSS) test for trend or mean stationarity, the Phillips-Perron (PP) test for the presence of a unit root and the White test for homoscedasticity--on an illustrative set of MEG data. For five stimulation sessions, we found already for short epochs of duration of 250 and 500 ms that, although the majority of the studied epochs of single MEG trials were usually mean-stationary (KPSS test and PP test), they were classified as nonstationary due to their heteroscedasticity (White test). We also observed that the presence of external auditory stimulation did not significantly affect the findings regarding the stationarity of the data. We conclude that the combination of these tests allows a refined analysis of the stationarity of MEG and EEG time series.     

Isolation of plant DNA: A fast,inexpensive, and reliable method

We describe here a simple method to isolate DNA of high molecular weight from a wide variety of plant materials, such as trees, herbaceous plants, cell suspension cultures, calli, seeds, dried embryos, ferns and lichens. The crucial step of the extraction is the use of an acidic extraction medium. When necessary, the sample was separated on a fast RPC-5 column providing us with highly purified DNA suitable not only for restriction endonuclease analyses but also for PCR experiments, RLFP analyses, or detection of adducts.     

A fast and reliable computational method for estimating population genetic parameters

The estimation of ancestral and current effective population sizes in expanding populations is a fundamental problem in population genetics. Recently it has become possible to scan entire genomes of several individuals within a population. These genomic data sets can be used to estimate basic population parameters such as the effective population size and population growth rate. Full-data-likelihood methods potentially offer a powerful statistical framework for inferring population genetic parameters. However, for large data sets, computationally intensive methods based upon full-likelihood estimates may encounter difficulties. First, the computational method may be prohibitively slow or difficult to implement for large data. Second, estimation bias may markedly affect the accuracy and reliability of parameter estimates, as suggested from past work on coalescent methods. To address these problems, a fast and computationally efficient least-squares method for estimating population parameters from genomic data is presented here. Instead of modeling genomic data using a full likelihood, this new approach uses an analogous function, in which the full data are replaced with a vector of summary statistics. Furthermore, these least-squares estimators may show significantly less estimation bias for growth rate and genetic diversity than a corresponding maximum-likelihood estimator for the same coalescent process. The least-squares statistics also scale up to genome-sized data sets with many nucleotides and loci. These results demonstrate that least-squares statistics will likely prove useful for nonlinear parameter estimation when the underlying population genomic processes have complex evolutionary dynamics involving interactions between mutation, selection, demography, and recombination.     

A review of EEG and MEG for brainnetome research

The majority of brain activities are performed by functionally integrating separate regions of the brain. Therefore, the synchronous operation of the brain’s multiple regions or neuronal assemblies can be represented as a network with nodes that are interconnected by links. Because of the complexity of brain interactions and their varying effects at different levels of complexity, one of the corresponding authors of this paper recently proposed the brainnetome as a new –ome to explore and integrate the brain network at different scales. Because electroencephalography (EEG) and magnetoencephalography (MEG) are noninvasive and have outstanding temporal resolution and because they are the primary clinical techniques used to capture the dynamics of neuronal connections, they lend themselves to the analysis of the neural networks comprising the brainnetome. Because of EEG/MEG’s applicability to brainnetome analyses, the aim of this review is to identify the procedures that can be used to form a network using EEG/MEG data in sensor or source space and to promote EEG/MEG network analysis for either neuroscience or clinical applications. To accomplish this aim, we show the relationship of the brainnetome to brain networks at the macroscale and provide a systematic review of network construction using EEG and MEG. Some potential applications of the EEG/MEG brainnetome are to use newly developed methods to associate the properties of a brainnetome with indices of cognition or disease conditions. Associations based on EEG/MEG brainnetome analysis may improve the comprehension of the functioning of the brain in neuroscience research or the recognition of abnormal patterns in neurological disease.     

A simple, fast and reliable method for obtaining dopamine histofluorescence from mesencephalic cultures

A modified glyoxylic acid technique for obtaining dopamine histofluorescence from cultured mesencephalic cells is described. This method requires only two solutions: one contains glyoxylic acid, sucrose and monobasic potassium phosphate and is used at room temperature, the other is a Hepes buffered solution used at 37 C. Relatively high concentrations of a monoamine oxidase inhibitor and dopamine are added to the cultures to load dopaminergic neurons; the cell bodies and their processes take up and hold dopamine quickly and evenly. The cultures are dipped in a glyoxylic acid solution, dried in air, heated for 5 min and coverslipped with mineral oil. Since the cultures remain in their culture dishes, the entire procedure takes less than 2 hr. The green histofluorescence characteristic of dopamine is seen when the cultures are viewed by standard fluorescence microscopy. Various cell body types and sizes can be distinguished, as well as the complete extent of their processes and varicosities.     

A fast top-down method for constructing reliable radiation hybrid frameworks

MOTIVATION: Radiation Hybrid Mapping (RHM) is a technique used to order a set of markers on a genome and estimating physical distances between them. RHM provides information on marker placement independent from other methods such as sequencing, and can therefore be used for example in genome sequencing to help ordering contigs. A radiation hybrid framework can be constructed by choosing a set of markers so that the chromosome coverage is good and so that the markers can be ordered with high confidence. Automatically constructing RHM frameworks is a computationally challenging problem. RESULTS: We have developed a new method for constructing radiation hybrid frameworks. Given a relatively large set of markers for a chromosome, the algorithm aims to select an ordered subset that makes up a framework, and that contains as many markers as possible. The algorithm has a time complexity that is better than any of the existing methods that we are aware of. Furthermore, we propose a method for comparing if two frameworks are consistent, giving a visual presentation as well as quantitative measures of how well the two frameworks agree. Applying our method on marker sets from 22 human chromosomes and comparing the resulting frameworks with previously published frameworks, we demonstrate that our automatic method efficiently constructs frameworks with good coverage of each chromosome and with high degree of agreement on the marker ordering.     

A fast, simple, and reliable high-yielding method for DNA extraction from different plant species

Genetic studies and pathogen detection in plants using molecular methods require the isolation of DNA from a large number of samples in a short time span. A rapid and versatile protocol for extracting high-quality DNA from different plant species is described. This method yields from 1 to 2 mg of DNA per gram of tissue. The absorbance ratios (A₂₆₀/A₂₈₀) obtained ranged from 1.6 to 2.0. A minimal presence of contaminating metabolites (as polymerase chain reaction [PCR] inhibitors) in samples and a considerable savings in reagents are characteristics of this protocol, as well as the low cost of the analysis per sample. The quality of the DNA was suitable for PCR amplification.     

Evolutionary optimization of classifiers and features for single-trial EEG Discrimination

Background  

State-of-the-art signal processing methods are known to detect information in single-trial event-related EEG data, a crucial aspect in development of real-time applications such as brain computer interfaces. This paper investigates one such novel approach, evaluating how individual classifier and feature subset tailoring affects classification of single-trial EEG finger movements. The discrete wavelet transform was used to extract signal features that were classified using linear regression and non-linear neural network models, which were trained and architecturally optimized with evolutionary algorithms. The input feature subsets were also allowed to evolve, thus performing feature selection in a wrapper fashion. Filter approaches were implemented as well by limiting the degree of optimization.     

Coupled oscillators for modeling and analysis of EEG/MEG oscillations.

This study presents three EEG/MEG applications in which the modeling of oscillatory signal components offers complementary analysis and an improved explanation of the underlying generator structures. Coupled oscillator networks were used for modeling. Parameters of the corresponding ordinary coupled differential equation (ODE) system are identified using EEG/MEG data and the resulting solution yields the modeled signals. This model-related analysis strategy provides information about the coupling quantity and quality between signal components (example 1, neonatal EEG during quiet sleep), allows identification of the possible contribution of hidden generator structures (example 2, 600-Hz MEG oscillations in somatosensory evoked magnetic fields), and can explain complex signal characteristics such as amplitude-frequency coupling and frequency entrainment (example 3, EEG burst patterns in sedated patients).     

Procedures for reliable estimation of viral fitness from time-series data

In order to develop a better understanding of the evolutionary dynamics of HIV drug resistance, it is necessary to quantify accurately the in vivo fitness costs of resistance mutations. However, the reliable estimation of such fitness costs is riddled with both theoretical and experimental difficulties. Experimental fitness assays typically suffer from the shortcoming that they are based on in vitro data. Fitness estimates based on the mathematical analysis of in vivo data, however, are often questionable because the underlying assumptions are not fulfilled. In particular, the assumption that the replication rate of the virus population is constant in time is frequently grossly violated. By extending recent work of Marée and colleagues, we present here a new approach that corrects for time-dependent viral replication in time-series data for growth competition of mutants. This approach allows a reliable estimation of the relative replicative capacity (with confidence intervals) of two competing virus variants growing within the same patient, using longitudinal data for the total plasma virus load, the relative frequency of the two variants and the death rate of infected cells. We assess the accuracy of our method using computer-generated data. An implementation of the developed method is freely accessible on the Web (http://www.eco.ethz.ch/fitness.html).     

A simple method for simultaneous estimation of zinc and copper in erythrocytes

A method is described for simultaneous estimation of zinc and copper in erythrocytes by hemolysis and flame aspiration atomic absorption spectrophotometry. Red blood cells (RBC) were also analyzed by the commonly used nitric acid digestion method for comparison. The difference in the results of zinc analyses of fifteen RBC samples by the two techniques was 0.5 ± 0.8 (mean ± SD) μg Zn/g hemoglobin indicating that these methods yield essentially similar results. Because of the low concentration of copper in RBC, results obtained by the acid digestion method were unreliable since nitric acid and undissolved particles of digested RBC in the acid extract increased instrumental noise to an unacceptable level. Average concentrations of zinc and copper estimated in RBC of 25 normal subjects by the present described technique (hemolysate method) were 43.9 and 2.0 μg/g Hb, respectively. No sex-related differences in RBC zinc or copper concentrations were found. The hemolysate method is simpler and faster to perform than the more commonly used nitric acid digestion method.     

A reliable method for the estimation of DNA in higher plant tissues.

A method for the isolation of the calcinogenic principle of Solanum malacoxylon is described. The procedure includes preliminary purification of an aqueous leaf extract by dialysis and treatment with ion-exchange resins. Final purification is achieved on Sephadex G-15 and G-10 columns and by paper chromatography.     

A method of evoking fast baroreceptor responses for the measurement of the baroreflex latency.

A method for measurement of latency in the baroreflex is described. Standardised square pressure pulse was applied to the isolated carotid sinus and simultaneous recordings of the carotid sinus nerve or sympathetic fibers were performed. Relatively short time of the increase of the pressure makes possible more exact measurements of latency in the baroreflex than other known methods used for this purpose.     

A fast, sensitive method for the simultaneous determination of alpha-tocopherol and alpha-tocopheryl acetate in mixed micelles

This report improves analytical procedures to investigate the behaviour of the two Vitamin E forms, alpha-tocopherol (Tol) and alpha-tocopheryl acetate (Tac), in model systems mimicking the intestinal medium. We describe how to prepare mixed micelles as vehicle for Tac and Tol and the HPLC method for their quantification in the micelles. Tac and Tol were extracted using ethanol-hexane-drying procedure, whereas the separation and detection were performed in methanol and by UV method, respectively. Both compounds were eluted in less than 4 min. In the range between 1.7 microM and 54 microM of Tac or Tol in the micelles, their recovery were 89% and 81%, respectively, with correlation coefficient over 0.99 and R.S.D. of less than 7.2% in all cases. Limits of detection and quantification for Tac and Tol in mixed micelles ranged between 1 microM and 2 microM and between 3 microM and 5 microM, respectively. The behaviours of Tac and Tol were quite different during the extraction procedure and both were influenced by the vitamin concentration and the relative volume of organic solvents.     

A reliable and simple method for simultaneous determination of DOPA and 3-O-methyldopa in plasma and brain

A rapid, simple, and reliable method for the simultaneous estimation of D and O-MD in plasma and brain is described. These compounds are eluted together, but separately from the catecholamines, by passing perchloric acid extracts through columns of a strong cation-exchange resin in the H⁺ form. The pH of the eluate is adjusted with the addition of a Na₃ citrate solution. Specific oxidation of D and O-MD are carried out by reacting with iodine and ferricyanide, respectively. No interference with plasma D and O-MD measurements was found from the presence in plasma of drugs commonly used in the treatment of parkinsonism. The presence of hydrazinomethyldopa and α-methyldopa partially interferes with the determinations of D and O-MD. Plasma levels of O-MD are greater than D in patients receiving chronic l-dopa therapy.