Brain-Computer Interface: comparison of two control modes to drive a virtual robot

A Brain-Computer Interface (BCI) is a system that enables communication and control that is not based on muscular movements, but on brain activity. Some of these systems are based on discrimination of different mental tasks; usually they match the number of mental tasks to the number of control commands. Previous research at the University of Málaga (UMA-BCI) have proposed a BCI system to freely control an external device, letting the subjects choose among several navigation commands using only one active mental task (versus any other mental activity). Although the navigation paradigm proposed in this system has been proved useful for continuous movements, if the user wants to move medium or large distances, he/she needs to keep the effort of the MI task in order to keep the command. In this way, the aim of this work was to test a navigation paradigm based on the brain-switch mode for ‘forward’ command. In this mode, the subjects used the mental task to switch their state on /off: they stopped if they were moving forward and vice versa. Initially, twelve healthy and untrained subjects participated in this study, but due to a lack of control in previous session, only four subjects participated in the experiment, in which they had to control a virtual robot using two paradigms: one based on continuous mode and another based on switch mode. Preliminary results show that both paradigms can be used to navigate through virtual environments, although with the first one the times needed to complete a path were notably lower.Universidad de Málaga. Campus de Excelencia Internacional Andalucía Tech

Exploring a P300 Brain-Computer Interface Based on Three Different RSVP Paradigms

A BCI Speller is a typical Brain-Computer Interface (BCI) system for communication purpose. This technology can provide users with severe motor disability with an assistive device controlled by brain activity. In the present preliminary study we investigated, in five subjects, the performance and the Information Transfer Rate (ITR) based on three different Rapid Serial Visual Presentation (RSVP) paradigms to control a BCI speller. The variants of the three paradigms were the stimuli presented: letters, images and famous faces. These preliminary results showed that performance can increase when using an RSVP paradigm based on images, and ITR can improves when using the images and the famous faces paradigms.Universidad de Málaga. Campus de Excelencia Internacional Andalucía Tech

Control de un teclado virtual por un paciente de ela mediante el uso de dos tecnologías: eyetracker y sistema BCI

Pacientes que sufren de Esclerosis Lateral Amiotrófica (ELA) pueden llegar a sufrir lo que se conoce como síndrome de enclaustramiento (Locked-in-syndrome, LIS), caracterizado, en su modalidad clásica, por la imposibilidad de realizar cualquier movimiento salvo parpadear y mover los ojos. Para estos pacientes, la tecnología asistida disponible es muy limitada, siendo aquellas basadas en el eyetracker (seguimiento de ojos) y en el BCI las más apropiadas.Varios estudios han tratado de comparar ambas tecnologías. En el caso de controlar un sistema de comunicación, estos concluyen que un eyetracker es más ventajoso. Precisamente, el objetivo del estudio que se propone en esta contribución es demostrar que el uso de la tecnología puede depender de las preferencias de cada usuario. Para ello se lleva a cabo un estudio comparativo entre el uso de un eyetracker (Tobii modelo C15) y una Interfaz Cerebro-Computadora basado en la detección del potencial P300 para controlar un teclado virtual. Dicho estudio se realiza sobre un paciente con ELA. El estudio de las prestaciones de ambos sistemas en términos de error y tiempo, además de la carga de trabajo y de otras medidas subjetivas, nos permitirán determinar la usabilidad de ambos sistemas y obtener resultados sobre dicha comparativaUniversidad de Málaga Campus de Excelencia Internacional Andalucía Tech

SynteBase/SynteView: a tool to visualize gene order conservation in prokaryotic genomes

<p>Abstract</p> <p>Background</p> <p>It has been repeatedly observed that gene order is rapidly lost in prokaryotic genomes. However, persistent synteny blocks are found when comparing more or less distant species. These genes that remain consistently adjacent are appealing candidates for the study of genome evolution and a more accurate definition of their functional role. Such studies require visualizing conserved synteny blocks in a large number of genomes at all taxonomic distances.</p> <p>Results</p> <p>After comparing nearly 600 completely sequenced genomes encompassing the whole prokaryotic tree of life, the computed synteny data were assembled in a relational database, SynteBase. SynteView was designed to visualize conserved synteny blocks in a large number of genomes after choosing one of them as a reference. SynteView functions with data stored either in SynteBase or in a home-made relational database of personal data. In addition, this software can compute <it>on-the-fly </it>and display the distribution of synteny blocks which are conserved in pairs of genomes. This tool has been designed to provide a wealth of information on each positional orthologous gene, to be user-friendly and customizable. It is also possible to download sequences of genes belonging to these synteny blocks for further studies. SynteView is accessible through Java Webstart at <url>http://www.synteview.u-psud.fr</url>.</p> <p>Conclusion</p> <p>SynteBase answers queries about gene order conservation and SynteView visualizes the obtained results in a flexible and powerful way which provides a comparative overview of the conserved synteny in a large number of genomes, whatever their taxonomic distances.</p

FUNGIpath: a tool to assess fungal metabolic pathways predicted by orthology

<p>Abstract</p> <p>Background</p> <p>More and more completely sequenced fungal genomes are becoming available and many more sequencing projects are in progress. This deluge of data should improve our knowledge of the various primary and secondary metabolisms of Fungi, including their synthesis of useful compounds such as antibiotics or toxic molecules such as mycotoxins. Functional annotation of many fungal genomes is imperfect, especially of genes encoding enzymes, so we need dedicated tools to analyze their metabolic pathways in depth.</p> <p>Description</p> <p>FUNGIpath is a new tool built using a two-stage approach. Groups of orthologous proteins predicted using complementary methods of detection were collected in a relational database. Each group was further mapped on to steps in the metabolic pathways published in the public databases KEGG and MetaCyc. As a result, FUNGIpath allows the primary and secondary metabolisms of the different fungal species represented in the database to be compared easily, making it possible to assess the level of specificity of various pathways at different taxonomic distances. It is freely accessible at <url>http://www.fungipath.u-psud.fr</url>.</p> <p>Conclusions</p> <p>As more and more fungal genomes are expected to be sequenced during the coming years, FUNGIpath should help progressively to reconstruct the ancestral primary and secondary metabolisms of the main branches of the fungal tree of life and to elucidate the evolution of these ancestral fungal metabolisms to various specific derived metabolisms.</p

Assessing the evolutionary rate of positional orthologous genes in prokaryotes using synteny data

<p>Abstract</p> <p>Background</p> <p>Comparison of completely sequenced microbial genomes has revealed how fluid these genomes are. Detecting synteny blocks requires reliable methods to determining the orthologs among the whole set of homologs detected by exhaustive comparisons between each pair of completely sequenced genomes. This is a complex and difficult problem in the field of comparative genomics but will help to better understand the way prokaryotic genomes are evolving.</p> <p>Results</p> <p>We have developed a suite of programs that automate three essential steps to study conservation of gene order, and validated them with a set of 107 bacteria and archaea that cover the majority of the prokaryotic taxonomic space. We identified the whole set of shared homologs between two or more species and computed the evolutionary distance separating each pair of homologs. We applied two strategies to extract from the set of homologs a collection of valid orthologs shared by at least two genomes. The first computes the Reciprocal Smallest Distance (RSD) using the PAM distances separating pairs of homologs. The second method groups homologs in families and reconstructs each family's evolutionary tree, distinguishing <it>bona fide </it>orthologs as well as paralogs created after the last speciation event. Although the phylogenetic tree method often succeeds where RSD fails, the reverse could occasionally be true. Accordingly, we used the data obtained with either methods or their intersection to number the orthologs that are adjacent in for each pair of genomes, the Positional Orthologous Genes (POGs), and to further study their properties. Once all these synteny blocks have been detected, we showed that POGs are subject to more evolutionary constraints than orthologs outside synteny groups, whichever the taxonomic distance separating the compared organisms.</p> <p>Conclusion</p> <p>The suite of programs described in this paper allows a reliable detection of orthologs and is useful for evaluating gene order conservation in prokaryotes whichever their taxonomic distance. Thus, our approach will make easy the rapid identification of POGS in the next few years as we are expecting to be inundated with thousands of completely sequenced microbial genomes.</p

ORENZA: a web resource for studying ORphan ENZyme activities

BACKGROUND: Despite the current availability of several hundreds of thousands of amino acid sequences, more than 36% of the enzyme activities (EC numbers) defined by the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (NC-IUBMB) are not associated with any amino acid sequence in major public databases. This wide gap separating knowledge of biochemical function and sequence information is found for nearly all classes of enzymes. Thus, there is an urgent need to explore these sequence-less EC numbers, in order to progressively close this gap. DESCRIPTION: We designed ORENZA, a PostgreSQL database of ORphan ENZyme Activities, to collate information about the EC numbers defined by the NC-IUBMB with specific emphasis on orphan enzyme activities. Complete lists of all EC numbers and of orphan EC numbers are available and will be periodically updated. ORENZA allows one to browse the complete list of EC numbers or the subset associated with orphan enzymes or to query a specific EC number, an enzyme name or a species name for those interested in particular organisms. It is possible to search ORENZA for the different biochemical properties of the defined enzymes, the metabolic pathways in which they participate, the taxonomic data of the organisms whose genomes encode them, and many other features. The association of an enzyme activity with an amino acid sequence is clearly underlined, making it easy to identify at once the orphan enzyme activities. Interactive publishing of suggestions by the community would provide expert evidence for re-annotation of orphan EC numbers in public databases. CONCLUSION: ORENZA is a Web resource designed to progressively bridge the unwanted gap between function (enzyme activities) and sequence (dataset present in public databases). ORENZA should increase interactions between communities of biochemists and of genomicists. This is expected to reduce the number of orphan enzyme activities by allocating gene sequences to the relevant enzymes

BRAIN-COMPUTER INTERFACE: COMPARISON OF TWO CONTROL MODES TO DRIVE A VIRTUAL ROBOT

A Brain-Computer Interface (BCI) is a system that enables communication and control that is not based on muscular movements, but on brain activity. Some of these systems are based on discrimination of different mental tasks; usually they match the number of mental tasks to the number of control commands. Previous research at the University of Málaga (UMABCI) have proposed a BCI system to freely control an external device, letting the subjects choose among several navigation commands using only one active mental task (versus any other mental activity). Although the navigation paradigm proposed in this system has been proved useful for continuous movements, if the user wants to move medium or large distances, he/she needs to keep the effort of the MI task in order to keep the command. In this way, the aim of this work was to test a navigation paradigm based on the brain-switch mode for ‘forward’ command. In this mode, the subjects used the mental task to switch their state on /off: they stopped if they were moving forward and vice versa. Initially, twelve healthy and untrained subjects participated in this study, but due to a lack of control in previous session, only four subjects participated in the experiment, in which they had to control a virtual robot using two paradigms: one based on continuous mode and another based on switch mode. Preliminary results show that both paradigms can be used to navigate through virtual environments, although with the first one the times needed to complete a path were notably lower

A survey of orphan enzyme activities

<p>Abstract</p> <p>Background</p> <p>Using computational database searches, we have demonstrated previously that no gene sequences could be found for at least 36% of enzyme activities that have been assigned an Enzyme Commission number. Here we present a follow-up literature-based survey involving a statistically significant sample of such "orphan" activities. The survey was intended to determine whether sequences for these enzyme activities are truly unknown, or whether these sequences are absent from the public sequence databases but can be found in the literature.</p> <p>Results</p> <p>We demonstrate that for ~80% of sampled orphans, the absence of sequence data is bona fide. Our analyses further substantiate the notion that many of these enzyme activities play biologically important roles.</p> <p>Conclusion</p> <p>This survey points toward significant scientific cost of having such a large fraction of characterized enzyme activities disconnected from sequence data. It also suggests that a larger effort, beginning with a comprehensive survey of all putative orphan activities, would resolve nearly 300 artifactual orphans and reconnect a wealth of enzyme research with modern genomics. For these reasons, we propose that a systematic effort to identify the cognate genes of orphan enzymes be undertaken.</p

BRAIN-COMPUTER INTERFACE: COMPARISON OF TWO CONTROL MODES TO DRIVE A VIRTUAL ROBOT

A Brain-Computer Interface (BCI) is a system that enables communication and control that is not based on muscular movements, but on brain activity. Some of these systems are based on discrimination of different mental tasks; usually they match the number of mental tasks to the number of control commands. Previous research at the University of Málaga (UMABCI) have proposed a BCI system to freely control an external device, letting the subjects choose among several navigation commands using only one active mental task (versus any other mental activity). Although the navigation paradigm proposed in this system has been proved useful for continuous movements, if the user wants to move medium or large distances, he/she needs to keep the effort of the MI task in order to keep the command. In this way, the aim of this work was to test a navigation paradigm based on the brain-switch mode for ‘forward’ command. In this mode, the subjects used the mental task to switch their state on /off: they stopped if they were moving forward and vice versa. Initially, twelve healthy and untrained subjects participated in this study, but due to a lack of control in previous session, only four subjects participated in the experiment, in which they had to control a virtual robot using two paradigms: one based on continuous mode and another based on switch mode. Preliminary results show that both paradigms can be used to navigate through virtual environments, although with the first one the times needed to complete a path were notably lower