Quick and efficient approach to develop genomic resources in orphan species: Application in Lavandula angustifolia.

Next-Generation Sequencing (NGS) technologies, by reducing the cost and increasing the throughput of sequencing, have opened doors to generate genomic data in a range of previously poorly studied species. In this study, we propose a method for the rapid development of a large-scale molecular resources for orphan species. We studied as an example the true lavender (Lavandula angustifolia Mill.), a perennial sub-shrub plant native from the Mediterranean region and whose essential oil have numerous applications in cosmetics, pharmaceuticals, and alternative medicines. The heterozygous clone "Maillette" was used as a reference for DNA and RNA sequencing. We first built a reference Unigene, compound of coding sequences, thanks to de novo RNA-seq assembly. Then, we reconstructed the complete genes sequences (with introns and exons) using an Unigene-guided DNA-seq assembly approach. This aimed to maximize the possibilities of finding polymorphism between genetically close individuals despite the lack of a reference genome. Finally, we used these resources for SNP mining within a collection of 16 commercial lavender clones and tested the SNP within the scope of a genetic distance analysis. We obtained a cleaned reference of 8, 030 functionally in silico annotated genes. We found 359K polymorphic sites and observed a high SNP frequency (mean of 1 SNP per 90 bp) and a high level of heterozygosity (more than 60% of heterozygous SNP per genotype). On overall, we found similar genetic distances between pairs of clones, which is probably related to the out-crossing nature of the species and the restricted area of cultivation. The proposed method is transferable to other orphan species, requires little bioinformatics resources and can be realized within a year. This is also the first reported large-scale SNP development on Lavandula angustifolia. All the genomics resources developed herein are publicly available and provide a rich pool of molecular resources to explore and exploit lavender genetic diversity in breeding programs.

Dual adaptive filtering by optimal projection applied to filter muscle artifacts on EEG and comparative study.

Muscle artifacts constitute one of the major problems in electroencephalogram (EEG) examinations, particularly for the diagnosis of epilepsy, where pathological rhythms occur within the same frequency bands as those of artifacts. This paper proposes to use the method dual adaptive filtering by optimal projection (DAFOP) to automatically remove artifacts while preserving true cerebral signals. DAFOP is a two-step method. The first step consists in applying the common spatial pattern (CSP) method to two frequency windows to identify the slowest components which will be considered as cerebral sources. The two frequency windows are defined by optimizing convolutional filters. The second step consists in using a regression method to reconstruct the signal independently within various frequency windows. This method was evaluated by two neurologists on a selection of 114 pages with muscle artifacts, from 20 clinical recordings of awake and sleeping adults, subject to pathological signals and epileptic seizures. A blind comparison was then conducted with the canonical correlation analysis (CCA) method and conventional low-pass filtering at 30 Hz. The filtering rate was 84.3% for muscle artifacts with a 6.4% reduction of cerebral signals even for the fastest waves. DAFOP was found to be significantly more efficient than CCA and 30 Hz filters. The DAFOP method is fast and automatic and can be easily used in clinical EEG recordings.

Evaluation of the AFOP/DAFOP method for automatic filtering of EEGs of patients with epilepsy.

OBJECTIVE: Further developments in EEG monitoring necessitate new methods of filtering to eliminate artifacts, without transforming relevant signals. This article presents an automatic filtering of EEG recordings, based on a spatio-temporal method called Adaptive Filtering by Optimal Projection or Dual Adaptive Filtering by Optimal Projection. Evaluation of filtering methods is difficult, and comparisons between methods remain a challenge; here, we present a method to score the visual assessment of the EEG. The aim of this study was to evaluate an automatic filtering method, called Adaptive Filtering by Optimal Projection, improved by Dual Adaptive Filtering by Optimal Projection, of EEG recordings of patients with epilepsy. METHODS: Two hundred forty-eight nonfiltered EEG segments of 20 seconds each were selected from 35 EEG recordings of 27 different patients by 3 clinical neurophysiologists based on their content. The reading quality as well as the proportions of artifacts and of cerebral activity removed after filtering were evaluated on a scale of 0 to 4. The mean square difference of amplitude before and after filtering was computed in specific spectral band. RESULTS: The artifacts were largely removed (82% for muscular, 72% for ocular, and 71% for electrode artifacts). The readability was improved on an average by two points for pages containing epileptic seizures, and by one point for those containing alpha rhythms, slow waves, and spikes. After filtering, consistency tests showed a consensus (Spearman correlation [0.69-0.79]) on the removal of the artifact versus loss of information. The spectral analysis showed equivalent results (0.16% mean square difference in the alpha band). CONCLUSIONS: Our filtering method is effective in removing artifacts without altering relevant signals. The significance is that we evaluated a new automated method of filtering EEG that is easy to use for both for the analysis of routine EEG and in the field of epilepsy at large.

BioSigPlot: an opensource tool for the visualization of multi-channel biomedical signals with Matlab.

This paper presents a Matlab-based software (MathWorks inc.) called BioSigPlot for the visualization of multi-channel biomedical signals, particularly for the EEG. This tool is designed for researchers on both engineering and medicine who have to collaborate to visualize and analyze signals. It aims to provide a highly customizable interface for signal processing experimentation in order to plot several kinds of signals while integrating the common tools for physician. The main advantages compared to other existing programs are the multi-dataset displaying, the synchronization with video and the online processing. On top of that, this program uses object oriented programming, so that the interface can be controlled by both graphic controls and command lines. It can be used as EEGlab plug-in but, since it is not limited to EEG, it would be distributed separately. BioSigPlot is distributed free of charge (http://biosigplot.sourceforge.net), under the terms of GNU Public License for non-commercial use and open source development.

Decrease of mutual information in brain electrical activity of patients with relapsing-remitting multiple sclerosis.

The disturbance of cortical communication has been hypothesized as an important factor in the appearance of cognitive impairment in (MS). Cortical communication is quantified here in control subjects and patients with relapsing-remitting multiple sclerosis (RRMS) on the basis of mean coherence in the δ, θ, α, ß and γ bands and using mutual information computed between pairs of bipolar EEG signals recorded during resting condition. Each patient received also a cognitive assessment using a battery of neuropsychological tests specific to cognitive deficits in MS. No difference was observed for the coherence indices whereas inter-hemispheric and right hemisphere mutual information is significantly lower in patients with MS than in control subjects. Moreover, inter-hemispheric mutual information decrease significantly with illness duration and right mutual information differentiate cognitively deficient and non-deficient patients. Mutual information allows to quantify the cortical communication in patients with RRMS and is related to clinical characteristics. Cortical communication quantified in a resting state might be a potential marker for the neurological damage induced by RRMS.

A global approach for automatic artifact removal for standard EEG record.

The EEG signal is a record of the brain activity using multiple electrodes placed on the scalp. Unfortunately, it can be hardly contaminated by a lot of noises called artifacts. These latter can be generated by various actions such as eye blinks, eye movements or the skeletal muscle activities (jaw, forehead, ...). This study will focus on a global artifact removal method using independent component analysis (ICA) on signals cut in frequency bands. The interest of this method resides in automatizing the artifactual source identification and enables a global filtering of records using constant bases. A brief overview of the project will be made in order to introduce the method used. Next, the results will be presented and their validation will be discussed in the conclusion.