Advances in blind source separation (BSS) and independent component analysis (ICA) for nonlinear mixtures

In this paper, we review recent advances in blind source separation (BSS) and independent component analysis (ICA) for nonlinear mixing models. After a general introduction to BSS and ICA, we discuss in more detail uniqueness and separability issues, presenting some new results. A fundamental difficulty in the nonlinear BSS problem and even more so in the nonlinear ICA problem is that they provide non-unique solutions without extra constraints, which are often implemented by using a suitable regularization. In this paper, we explore two possible approaches. The first one is based on structural constraints. Especially, post-nonlinear mixtures are an important special case, where a nonlinearity is applied to linear mixtures. For such mixtures, the ambiguities are essentially the same as for the linear ICA or BSS problems. The second approach uses Bayesian inference methods for estimating the best statistical parameters, under almost unconstrained models in which priors can be easily added. In the later part of this paper, various separation techniques proposed for post-nonlinear mixtures and general nonlinear mixtures are reviewed.     

Blind source separation and the analysis of microarray data.

We develop an approach for the exploratory analysis of gene expression data, based upon blind source separation techniques. This approach exploits higher-order statistics to identify a linear model for (logarithms of) expression profiles, described as linear combinations of "independent sources." As a result, it yields "elementary expression patterns" (the "sources"), which may be interpreted as potential regulation pathways. Further analysis of the so-obtained sources show that they are generally characterized by a small number of specific coexpressed or antiexpressed genes. In addition, the projections of the expression profiles onto the estimated sources often provides significant clustering of conditions. The algorithm relies on a large number of runs of "independent component analysis" with random initializations, followed by a search of "consensus sources." It then provides estimates for independent sources, together with an assessment of their robustness. The results obtained on two datasets (namely, breast cancer data and Bacillus subtilis sulfur metabolism data) show that some of the obtained gene families correspond to well known families of coregulated genes, which validates the proposed approach.     

Testing of instantaneity hypothesis for blind source separation of extensor indicis and extensor digiti minimi surface electromyograms

Human muscle activity can be assessed with surface electromyography (SEMG). Depending on electrode location and size, the recording volume under the sensor is likely to measure electrical potentials emanating from muscles other than the muscle of interest. This crosstalk issue makes interpretation of SEMG data difficult. The purpose of this paper was to study a crosstalk reduction technique called blind source separation (BSS). Most straightforward separation techniques rely on linearity and instantaneity (LI) of signal mixtures on the sensors. Literature on BSS for SEMG often makes hypothesis of linearity and instantaneity of the mixing model. Using simulation of SEMG mixtures and real SEMG recordings on the human extensor indicis (EI) and extensor digiti minimi (EDM) muscles during a task consisting of selective successive activations of EI and EDM muscles, cross-correlation between the sensors was proven to be directly dependent on instantaneity of the sources. Instantaneity hypothesis testing on real SEMG recordings showed that source instantaneity hypothesis is very sensitive to electrode location along the fibers direction. Source separation gains using JADE BSS algorithm depend strongly on instantaneity hypothesis. Using LI BSS on SEMG requires great attention to electrode positioning; we provide a tool to test these on EI/EDM muscles.     

Effectiveness of Ginkgo biloba in treating tinnitus: double blind, placebo controlled trial

ObjectiveTo determine whether Ginkgo biloba is effective in treating tinnitus.DesignDouble blind, placebo controlled trial using postal questionnaires.Participants1121 healthy people aged between 18 and 70 years with tinnitus that was comparatively stable; 978 participants were matched (489 pairs).Intervention12 weeks'' treatment with either 50 mg Ginkgo biloba extract LI 1370 three times daily or placebo.ResultsThere were no significant differences in primary or secondary outcome measures between the groups. 34 of 360 participants receiving active treatment reported that their tinnitus was less troublesome after 12 weeks of treatment compared with 35 of 360 participants who took placebo.Conclusions50 mg Ginkgo biloba extract LI 1370 given 3 times daily for 12 weeks is no more effective than placebo in treating tinnitus.     

Copasetic analysis: a framework for the blind analysis of microarray imagery

From its conception, bioinformatics has been a multidisciplinary field which blends domain expert knowledge with new and existing processing techniques, all of which are focused on a common goal. Typically, these techniques have focused on the direct analysis of raw microarray image data. Unfortunately, this fails to utilise the image's full potential and in practice, this results in the lab technician having to guide the analysis algorithms. This paper presents a dynamic framework that aims to automate the process of microarray image analysis using a variety of techniques. An overview of the entire framework process is presented, the robustness of which is challenged throughout with a selection of real examples containing varying degrees of noise. The results show the potential of the proposed framework in its ability to determine slide layout accurately and perform analysis without prior structural knowledge. The algorithm achieves approximately, a 1 to 3 dB improved peak signal-to-noise ratio compared to conventional processing techniques like those implemented in GenePix when used by a trained operator. As far as the authors are aware, this is the first time such a comprehensive framework concept has been directly applied to the area of microarray image analysis.     

The differences in brain activity between narrow band noise and pure tone tinnitus

Background

Tinnitus is an auditory sensation characterized by the perception of sound or noise in the absence of any external sound source. Based on neurobiological research, it is generally accepted that most forms of tinnitus are attributable to maladaptive plasticity due to damage to auditory system. Changes have been observed in auditory structures such as the inferior colliculus, the thalamus and the auditory cortex as well as in non-auditory brain areas. However, the observed changes show great variability, hence lacking a conclusive picture. One of the reasons might be the selection of inhomogeneous groups in data analysis.

Methodology

The aim of the present study was to delineate the differences between the neural networks involved in narrow band noise and pure tone tinnitus conducting LORETA based source analysis of resting state EEG.

Conclusions

Results demonstrated that narrow band noise tinnitus patients differ from pure tone tinnitus patients in the lateral frontopolar (BA 10), PCC and the parahippocampal area for delta, beta and gamma frequency bands, respectively. The parahippocampal-PCC current density differences might be load dependent, as noise-like tinnitus constitutes multiple frequencies in contrast to pure tone tinnitus. The lateral frontopolar differences might be related to pitch specific memory retrieval.     

Hemin toxicity: a preventable source of brain damage following hemorrhagic stroke

Abstract

Hemorrhagic stroke is a common cause of permanent brain damage, with a significant amount of the damage occurring in the weeks following a stroke. This secondary damage is partly due to the toxic effects of hemin, a breakdown product of hemoglobin. The serum proteins hemopexin and albumin can bind hemin, but these natural defenses are insufficient to cope with the extremely high amounts of hemin (10 mM) that can potentially be liberated from hemoglobin in a hematoma. The present review discusses how hemin gets into brain cells, and examines the multiple routes through which hemin can be toxic. These include the release of redox-active iron, the depletion of cellular stores of NADPH and glutathione, the production of superoxide and hydroxyl radicals, and the peroxidation of membrane lipids. Important gaps are revealed in contemporary knowledge about the metabolism of hemin by brain cells, particularly regarding how hemin interacts with hydrogen peroxide. Strategies currently being developed for the reduction of hemin toxicity after hemorrhagic stroke include chelation therapy, antioxidant therapy and the modulation of heme oxygenase activity. Future strategies may be directed at preventing the uptake of hemin into brain cells to limit the opportunity for toxic interactions.     

Outbreak of acute histoplasmosis in a family group: identification of the infection source

An outbreak of acute histoplasmosis occurring in 4 members of the same family, two women, a girl and a male, is reported. The index case presented acute respiratory symptoms, severe enough to require hospitalization. In the remaining persons, the infection was asymptomatic but was evidenced by reactive histoplasmin serologic tests. Search for the common source of infection led to an enriched soil obtained in a local nursery for growing in-door plants. BALB/c mice were inoculated with suspensions of soils from the potted plants. Histoplasma capsulatum var. capsulatum was isolated from various internal organs of the mice. Although histoplasmosis is observed more frequently in persons with occupations implying risk of exposure and is connected to rural areas, outbreaks and intra-family cases are now common in urban areas. This is due to massive urbanization, deforestation, demolitions and the use of soils enriched with organic compounds, mainly bird/bat excrements. This report calls the attention on the danger involved in using such enriched soils for plant nutrition.     

The source of choline for acetylcholine synthesis in brain

More is known about the synthesis and metabolism of acetylcholine (ACh) than other choline (Ch) containing compounds in the brain in spite of the fact that ACh represents only a small fraction of the total Ch esters. This review will attempt to summarize the evidence for the source of Ch in the brain and its relation to the turnover of ACh. Ch is a precursor not only for ACh but also for phosphoryl Ch and phospholipids. It appears that in the rat a bound form of Ch in the brain can produce free Ch which can leave the brain, be converted to ACh or be reutilized for phospholipid synthesis. There is evidence that one of the sources of free Ch that is utilized for ACh synthesis is outside the cholinergic nerve terminal.     

Partitioning the proteome: phase separation for targeted analysis of membrane proteins in human post-mortem brain

Neuroproteomics is a powerful platform for targeted and hypothesis driven research, providing comprehensive insights into cellular and sub-cellular disease states, Gene × Environmental effects, and cellular response to medication effects in human, animal, and cell culture models. Analysis of sub-proteomes is becoming increasingly important in clinical proteomics, enriching for otherwise undetectable proteins that are possible markers for disease. Membrane proteins are one such sub-proteome class that merit in-depth targeted analysis, particularly in psychiatric disorders. As membrane proteins are notoriously difficult to analyse using traditional proteomics methods, we evaluate a paradigm to enrich for and study membrane proteins from human post-mortem brain tissue. This is the first study to extensively characterise the integral trans-membrane spanning proteins present in human brain. Using Triton X-114 phase separation and LC-MS/MS analysis, we enriched for and identified 494 membrane proteins, with 194 trans-membrane helices present, ranging from 1 to 21 helices per protein. Isolated proteins included glutamate receptors, G proteins, voltage gated and calcium channels, synaptic proteins, and myelin proteins, all of which warrant quantitative proteomic investigation in psychiatric and neurological disorders. Overall, our sub-proteome analysis reduced sample complexity and enriched for integral membrane proteins by 2.3 fold, thus allowing for more manageable, reproducible, and targeted proteomics in case vs. control biomarker studies. This study provides a valuable reference for future neuroproteomic investigations of membrane proteins, and validates the use Triton X-114 detergent phase extraction on human post mortem brain.     

A new method for the extraction of fetal ECG from the dependent abdominal signals using blind source separation and adaptive noise cancellation techniques

Background

The electrocardiogram (ECG) is a diagnostic tool that records the electrical activity of the heart, and depicts it as a series of graph-like tracings, or waves. Being able to interpret these details allows diagnosis of a wide range of heart problems. Fetal electrocardiogram (FECG) extraction has an important impact in medical diagnostics during the mother pregnancy period. Since the observed FECG signals are often mixed with the maternal ECG (MECG) and the noise induced by the movement of electrodes or by mother motion, the separation process of the ECG signal sources from the observed data becomes quite complicated. One of its complexity is when the ECG sources are dependent, thus, in this paper we introduce a new approach of blind source separation (BSS) in the noisy context for both independent and dependent ECG signal source. This approach consist in denoising the observed ECG signals using a bilateral total variation (BTV) filter; then minimizing the Kullbak-Leibler divergence between copula densities to separate the FECG signal from the MECG one.

Results

We present simulation results illustrating the performance of our proposed method. We will consider many examples of independent/dependent source component signals. The results will be compared with those of the classical method called independent component analysis (ICA) under the same conditions. The accuracy of source estimation is evaluated through a criterion, called again the signal-to-noise-ratio (SNR). The first experiment shows that our proposed method gives accurate estimation of sources in the standard case of independent components, with performance around 27 dB in term of SNR. In the second experiment, we show the capability of the proposed algorithm to successfully separate two noisy mixtures of dependent source components - with classical criterion devoted to the independent case - fails, and that our method is able to deal with the dependent case with good performance.

Conclusions

In this work, we focus specifically on the separation of the ECG signal sources taken from skin two electrodes located on a pregnant woman’s body. The ECG separation is interpreted as a noisy linear BSS problem with instantaneous mixtures. Firstly, a denoising step is required to reduce the noise due to motion artifacts using a BTV filter as a very effective one-pass filter for denoising. Then, we use the Kullbak-Leibler divergence between copula densities to separate the fetal heart rate from the mother one, for both independent and dependent cases.

     

The evolution of brain lateralization: a game-theoretical analysis of population structure

In recent years, it has become apparent that behavioural and brain lateralization at the population level is the rule rather than the exception among vertebrates. The study of these phenomena has so far been the province of neurology and neuropsychology. Here, we show how such research can be integrated with evolutionary biology to understand lateralization more fully. In particular, we address the fact that, within a species, left- and right-type individuals often occur in proportions different from one-half (e.g. hand use in humans). The traditional explanations offered for lateralization of brain function (that it may avoid unnecessary duplication of neural circuitry and reduce interference between functions) cannot account for this fact, because increased individual efficiency is unrelated to the alignment of lateralization at the population level. A further puzzle is that such an alignment may even be disadvantageous, as it makes individual behaviour more predictable to other organisms. Here, we show that alignment of the direction of behavioural asymmetries in a population can arise as an evolutionarily stable strategy when individual asymmetrical organisms must coordinate their behaviour with that of other asymmetrical organisms. Brain and behavioural lateralization, as we know it in humans and other vertebrates, may have evolved under basically 'social' selection pressures.     

Blind source separation,wavelet denoising and discriminant analysis for EEG artefacts and noise cancelling

This paper proposes an automatic method for artefact removal and noise elimination from scalp electroencephalogram recordings (EEG). The method is based on blind source separation (BSS) and supervised classification and proposes a combination of classical and news features and classes to improve artefact elimination (ocular, high frequency muscle and ECG artefacts). The role of a supplementary step of wavelet denoising (WD) is explored and the interactions between BSS, denoising and classification are analyzed. The results are validated on simulated signals by quantitative evaluation criteria and on real EEG by medical expertise. The proposed methodology successfully rejected a good percentage of artefacts and noise, while preserving almost all the cerebral activity. The “denoised artefact-free” EEG presents a very good improvement compared with recorded raw EEG: 96% of the EEGs are easier to interpret.     

The dried corncob as a source of DNA for PCR analysis

We developed a procedure to isolate DNA from dried corncobs. This DNA was amplified successfully by PCR, producing well-defined bands in response to specific primers. The SSR patterns between cob and leaf DNA of the same inbred line were found to be identical, indicating that the DNA in the cob cells had not degraded during senescence.