Submillimeter three-dimensional coronary MR angiography with real-time navigator correction: comparison of navigator locations.

Three-dimensional free-breathing coronary magnetic resonance angiography was performed in eight healthy volunteers with use of real-time navigator technology. Images acquired with the navigator localized at the right hemidiaphragm and at the left ventricle were objectively compared. The diaphragmatic navigator was found to be superior for vessel delineation of middle to distal portions of the coronary arteries.

Rapid and selective surveillance of Arabidopsis thaliana genome annotations with Centrifuge.

Centrifuge is a user-friendly system to simultaneously access Arabidopsis gene annotations and intra- and inter-organism sequence comparison data. The tool allows rapid retrieval of user-selected data for each annotated Arabidopsis gene providing, in any combination, data on the following features: predicted protein properties such as mass, pI, cellular location and transmembrane domains; SWISS-PROT annotations; Interpro domains; Gene Ontology records; verified transcription; BLAST matches to the proteomes of A.thaliana, Oryza sativa (rice), Caenorhabditis elegans, Drosophila melanogaster and Homo sapiens. The tool lends itself particularly well to the rapid analysis of contigs or of tens or hundreds of genes identified by high-throughput gene expression experiments. In these cases, a summary table of principal predicted protein features for all genes is given followed by more detailed reports for each individual gene. Centrifuge can also be used for single gene analysis or in a word search mode. AVAILABILITY: http://centrifuge.unil.ch/ CONTACT: edward.farmer@unil.ch.

The Gene Ontology in 2010: extensions and refinements.

The Gene Ontology (GO) Consortium (http://www.geneontology.org) (GOC) continues to develop, maintain and use a set of structured, controlled vocabularies for the annotation of genes, gene products and sequences. The GO ontologies are expanding both in content and in structure. Several new relationship types have been introduced and used, along with existing relationships, to create links between and within the GO domains. These improve the representation of biology, facilitate querying, and allow GO developers to systematically check for and correct inconsistencies within the GO. Gene product annotation using GO continues to increase both in the number of total annotations and in species coverage. GO tools, such as OBO-Edit, an ontology-editing tool, and AmiGO, the GOC ontology browser, have seen major improvements in functionality, speed and ease of use.

ABS: a database of Annotated regulatory Binding Sites from orthologous promoters

Information about the genomic coordinates and the sequence of experimentally identified transcription factor binding sites is found scattered under a variety of diverse formats. The availability of standard collections of such high-quality data is important to design, evaluate and improve novel computational approaches to identify binding motifs on promoter sequences from related genes. ABS (http://genome.imim.es/datasets/abs2005/index.html) is a public database of known binding sites identified in promoters of orthologous vertebrate genes that have been manually curated from bibliography. We have annotated 650 experimental binding sites from 68 transcription factors and 100 orthologous target genes in human, mouse, rat or chicken genome sequences. Computational predictions and promoter alignment information are also provided for each entry. A simple and easy-to-use web interface facilitates data retrieval allowing different views of the information. In addition, the release 1.0 of ABS includes a customizable generator of artificial datasets based on the known sites contained in the collection and an evaluation tool to aid during the training and the assessment of motif-finding programs.

CleanEx: a database of heterogeneous gene expression data based on a consistent gene nomenclature.

The main goal of CleanEx is to provide access to public gene expression data via unique gene names. A second objective is to represent heterogeneous expression data produced by different technologies in a way that facilitates joint analysis and cross-data set comparisons. A consistent and up-to-date gene nomenclature is achieved by associating each single experiment with a permanent target identifier consisting of a physical description of the targeted RNA population or the hybridization reagent used. These targets are then mapped at regular intervals to the growing and evolving catalogues of human genes and genes from model organisms. The completely automatic mapping procedure relies partly on external genome information resources such as UniGene and RefSeq. The central part of CleanEx is a weekly built gene index containing cross-references to all public expression data already incorporated into the system. In addition, the expression target database of CleanEx provides gene mapping and quality control information for various types of experimental resource, such as cDNA clones or Affymetrix probe sets. The web-based query interfaces offer access to individual entries via text string searches or quantitative expression criteria. CleanEx is accessible at: http://www.cleanex.isb-sib.ch/.

The M-Coffee web server: a meta-method for computing multiple sequence alignments by combining alternative alignment methods.

The M-Coffee server is a web server that makes it possible to compute multiple sequence alignments (MSAs) by running several MSA methods and combining their output into one single model. This allows the user to simultaneously run all his methods of choice without having to arbitrarily choose one of them. The MSA is delivered along with a local estimation of its consistency with the individual MSAs it was derived from. The computation of the consensus multiple alignment is carried out using a special mode of the T-Coffee package [Notredame, Higgins and Heringa (T-Coffee: a novel method for fast and accurate multiple sequence alignment. J. Mol. Biol. 2000; 302: 205-217); Wallace, O'Sullivan, Higgins and Notredame (M-Coffee: combining multiple sequence alignment methods with T-Coffee. Nucleic Acids Res. 2006; 34: 1692-1699)] Given a set of sequences (DNA or proteins) in FASTA format, M-Coffee delivers a multiple alignment in the most common formats. M-Coffee is a freeware open source package distributed under a GPL license and it is available either as a standalone package or as a web service from www.tcoffee.org.

Using Digital Video Analysis to Monitor Driver Behavior at Intersections

Commercially available instruments for road-side data collection take highly limited measurements, require extensive manual input, or are too expensive for widespread use. However, inexpensive computer vision techniques for digital video analysis can be applied to automate the monitoring of driver, vehicle, and pedestrian behaviors. These techniques can measure safety-related variables that cannot be easily measured using existing sensors. The use of these techniques will lead to an improved understanding of the decisions made by drivers at intersections. These automated techniques allow the collection of large amounts of safety-related data in a relatively short amount of time. There is a need to develop an easily deployable system to utilize these new techniques. This project implemented and tested a digital video analysis system for use at intersections. A prototype video recording system was developed for field deployment. A computer interface was implemented and served to simplify and automate the data analysis and the data review process. Driver behavior was measured at urban and rural non-signalized intersections. Recorded digital video was analyzed and used to test the system.

Multi-slice three-dimensional myocardial strain tensor quantification using zHARP.

In this article we propose a novel method for calculating cardiac 3-D strain. The method requires the acquisition of myocardial short-axis (SA) slices only and produces the 3-D strain tensor at every point within every pair of slices. Three-dimensional displacement is calculated from SA slices using zHARP which is then used for calculating the local displacement gradient and thus the local strain tensor. There are three main advantages of this method. First, the 3-D strain tensor is calculated for every pixel without interpolation; this is unprecedented in cardiac MR imaging. Second, this method is fast, in part because there is no need to acquire long-axis (LA) slices. Third, the method is accurate because the 3-D displacement components are acquired simultaneously and therefore reduces motion artifacts without the need for registration. This article presents the theory of computing 3-D strain from two slices using zHARP, the imaging protocol, and both phantom and in-vivo validation.

Inducing illusory ownership of a virtual body

We discuss three experiments that investigate how virtual limbs and bodies can come to feel like real limbs and bodies. The fi rst experiment shows that an illusion of ownership of a virtual arm appearing to project out of a person"s shoulder can be produced by tactile stimulation on a person"s hidden real hand and synchronous stimulation on the seen virtual hand. The second shows that the illusion can be produced by synchronous movement of the person"s hidden real hand and a virtual hand. The third shows that a weaker form of the illusion can be produced when a brain-computer interface is employed to move the virtual hand by means of motor imagery without any tactile stimulation. We discuss related studies that indicate that the ownership illusion may be generated for an entire body. This has important implications for the scientific understanding of body ownership and several practical applications.

L'informatique: un outil remarquable pour l'enseignement de la médecine interne générale [The informatics: a remarkable tool for teaching general internal medicine].

INTERMED training implies a three week course, integrated in the "primary care module" for medical students in the first master year at the school of medicine in Lausanne. INTERMED uses an innovative teaching method based on repetitive sequences of e-learning-based individual learning followed by collaborative learning activities in teams, named Team-based learning (TBL). The e-learning takes place in a web-based virtual learning environment using a series of interactive multimedia virtual patients. By using INTERMED students go through a complete medical encounter applying clinical reasoning and choosing the diagnostic and therapeutic approach. INTERMED offers an authentic experience in an engaging and safe environment where errors are allowed and without consequences.

Towards a lightweight adaptative multicomponential affective recognition system

As part of the Affective Computing research field, the development of automatic affective recognition systems can enhance human-computer interactions by allowing the creation of interfaces that react to the user's emotional state. To that end, this Master Thesis brings affect recognition to nowadays most used human computer interface, mobile devices, by developing a facial expression recognition system able to perform detection under the difficult conditions of viewing angle and illumination that entails the interaction with a mobile device. Moreover, this Master Thesis proposes to combine emotional features detected from expression with contextual information of the current situation, to infer a complex and extensive emotional state of the user. Thus, a cognitive computational model of emotion is defined that provides a multicomponential affective state of the user through the integration of the detected emotional features into appraisal processes. In order to account for individual differences in the emotional experience, these processes can be adapted to the culture and personality of the user.

Control of Robot by Means of Human Thought

Brain computer interface (BCI) is a kind of human machine interface, which provides a new interaction method between human and computer or other equipment. The most significant characteristic of BCI system is that its control input is brain electrical activities acquired from the brain instead of traditional input such as hands or eyes. BCI technique has rapidly developed during last two decades and it has mainly worked as an auxiliary technique to help the disable people improve their life qualities. With the appearance of low cost novel electrical devices such as EMOTIV, BCI technique has been applied to the general public through many useful applications including video gaming, virtual reality and virtual keyboard. The purpose of this research is to be familiar with EMOTIV EPOC system and make use of it to build an EEG based BCI system for controlling an industrial manipulator by means of human thought. To build a BCI system, an acquisition program based on EMOTIV EPOC system is designed and a MFC based dialog that works as an operation panel is presented. Furthermore, the inverse kinematics of RV-3SB industrial robot was solved. In the last part of this research, the designed BCI system with human thought input is examined and the results indicate that the system is running smoothly and displays clearly the motion type and the incremental displacement of the motion.

Facilitating Mechanical Design with Augmented Reality

By enhancing a real scene with computer generated objects, Augmented Reality (AR), has proven itself as a valuable Human-Computer Interface (HCI) in numerous application areas such as medical, military, entertainment and manufacturing. It enables higher performance of on-site tasks with seamless presentation of up-to-date, task-related information to the users during the operation. AR has potentials in design because the current interface provided by Computer-aided Design (CAD) packages is less intuitive and reports show that the presence of physical objects help design thinking and communication. This research explores the use of AR to improve the efficiency of a design process, specifically in mechanical design.