Extraction of Vessels Networks over an Orientation Domain

This paper presents a new method to extract a network of vessels centerlines from a medical image. The network is composed of local geodesics over a four-dimensional space that includes local orientation and scale. These shortest paths follow closely the center of vessels and can deal robustly with crossings over the image plane. The vessel network is grown by an iterative algorithm that distributes seed points according to a geodesic saliency field. Numerical experiments on a database of synthetic and medical images show the superiority of our approach with respect to several methods based on shortest paths extractions. % With a minimum of user interaction, it allows to compute a complex network of vessels over noisy medical images

Extraction of Tubular Structures over an Orientation Domain

International audienceThis paper presents a new method to extract tubular structures from bi-dimensional images. The core of the proposed algorithm is the computation of geodesic curves over a four-dimensional space that includes local orientation and scale. These shortest paths follow closely the centerline of tubular structures, provide an estimation of the radius and can deal robustly with crossings over the image plane. Numerical experiments on a database of synthetic and natural images show the superiority of the proposed approach with respect to several method based on shortest paths extractions

Reliability of P mode event classification using contemporaneous BiSON and GOLF observations

We carried out a comparison of the signals seen in contemporaneous BiSON and GOLF data sets. Both instruments perform Doppler shift velocity measurements in integrated sunlight, although BiSON perform measurements from the two wings of potassium absorption line and GOLF from one wing of the NaD1 line. Discrepancies between the two datasets have been observed. We show,in fact, that the relative power depends on the wing in which GOLF data observes. During the blue wing period, the relative power is much higher than in BiSON datasets, while a good agreement has been observed during the red period.Comment: 7 pages, HELAS II: Helioseismology, Asteroseismology, and MHD Connections, conference proceedin

Monitoring temperate glaciers: combined use of multi-date TerraSAR-X images and continous GPS measurements

International audienceThis paper highlights the contribution of TerraSAR-X (TSX) High Resolution (HR) images for temperate glacier monitoring. A series of 14 images have been acquired since October 2007 on the Mont-Blanc test area. This area involves well-known temperate glaciers which have been monitored and instrumented ("stick" for annual displacement/ablation, GPS, cavitometer for basal displacement...) for more than 50 years. The combined use of in-situ measurements and multi-temporal images allows to improve the potential of HR SAR measurements. Interpretation of HR images, investigation of interferometric and correlation methods, and the first glacier displacement results are presented

Bioinformatic flowchart and database to investigate the origins and diversity of Clan AA peptidases

<p>Abstract</p> <p>Background</p> <p>Clan AA of aspartic peptidases relates the family of pepsin monomers evolutionarily with all dimeric peptidases encoded by eukaryotic LTR retroelements. Recent findings describing various pools of single-domain nonviral host peptidases, in prokaryotes and eukaryotes, indicate that the diversity of clan AA is larger than previously thought. The ensuing approach to investigate this enzyme group is by studying its phylogeny. However, clan AA is a difficult case to study due to the low similarity and different rates of evolution. This work is an ongoing attempt to investigate the different clan AA families to understand the cause of their diversity.</p> <p>Results</p> <p>In this paper, we describe in-progress database and bioinformatic flowchart designed to characterize the clan AA protein domain based on all possible protein families through ancestral reconstructions, sequence logos, and hidden markov models (HMMs). The flowchart includes the characterization of a major consensus sequence based on 6 amino acid patterns with correspondence with Andreeva's model, the structural template describing the clan AA peptidase fold. The set of tools is work in progress we have organized in a database within the GyDB project, referred to as Clan AA Reference Database <url>http://gydb.uv.es/gydb/phylogeny.php?tree=caard</url>.</p> <p>Conclusion</p> <p>The pre-existing classification combined with the evolutionary history of LTR retroelements permits a consistent taxonomical collection of sequence logos and HMMs. This set is useful for gene annotation but also a reference to evaluate the diversity of, and the relationships among, the different families. Comparisons among HMMs suggest a common ancestor for all dimeric clan AA peptidases that is halfway between single-domain nonviral peptidases and those coded by <it>Ty3/Gypsy </it>LTR retroelements. Sequence logos reveal how all clan AA families follow similar protein domain architecture related to the peptidase fold. In particular, each family nucleates a particular consensus motif in the sequence position related to the flap. The different motifs constitute a network where an alanine-asparagine-like variable motif predominates, instead of the canonical flap of the HIV-1 peptidase and closer relatives.</p> <p>Reviewers</p> <p>This article was reviewed by Daniel H. Haft, Vladimir Kapitonov (nominated by Jerry Jurka), and Ben M. Dunn (nominated by Claus Wilke).</p

Self-report psychopathy-III facet scores predict sexual crimes, sexual preferences, and sexual deviance index validity more precisely than total scores

Understanding the profiles of sexual offenders, such as the presence of psychopathic traits, is key to preventing future sexual crimes. The self-report psychopathy-III (SRP-III) is a tool used to assess the characteristics of psychopathy, but improvements on its interpretation are required to maximize its precision. The SRP-III can be interpreted by examining the scores on each of the four facets (interpersonal manipulation, callous affect, erratic lifestyle, antisocial behavior), on each of two factors (factor 1, factor 2), or by examining the total score. Here, we investigate the interpretation of the results from the SRP-III using these three approaches of analysis of the data for predicting types of sexual crimes, sexually deviant preferences (measured via PPG), and the validity of the sexual deviance results. Logistic regressions were carried out using either the four facets, two factors, or the total score of the SRP-III. Data were previously obtained from 198 Canadian men who were convicted of, or who admitted to committing, at least one sexual crime, or who reported experiencing sexually deviant fantasies. We also examined the point-biserial correlations between each of the methods of interpreting the SRP-III results and each of the dependent variables. We find that SRP-III facet scores most precisely predict types of sexual crimes, sexually deviant preferences, and sexual deviance index validity, followed by SRP-III factor scores, and lastly SRP-III total scores. Additionally, significant correlations are only found between SRP-III scores and one dependent variable. Potential reasons for this are discussed. Based on these findings, we recommend that future studies consider facet and factor scores in addition to the standard practice of examining total scores

Détection de la somnolence au volant par ECG obtenu par des capteurs textiles capacitifs non intrusifs

Les accidents de la route représentent une problématique majeure, engendrant un coût social de 1 000 dollars par habitant au Canada en 2020, soit 2 % du PIB national. Bien que les avancées technologiques et législatives aient permis de réduire significativement le nombre de décès entre 1973 et 2013, une tendance préoccupante à la hausse des accidents mortels est apparue depuis 2017. Parmi les causes identifiées, la fatigue se distingue par son implication dans 24 % des accidents mortels au Québec, demeurant l’un des facteurs les plus difficiles à détecter de manière fiable. Face à cette difficulté, les données physiologiques, notamment l’électrocardiogramme (ECG), se révèlent prometteuses pour détecter l’état de somnolence. Cependant, leur application dans des conditions réelles reste freinée par des limitations techniques, telles que la qualité des signaux captés de manière capacitive ou l’invasivité des dispositifs traditionnels. C’est dans ce contexte que cette recherche propose d’explorer la faisabilité d’un système non invasif de détection de la somnolence basé sur un ECG capacitif intégré au siège de conduite. Pour répondre à cet objectif, un système textile capacitif, comportant trois paires d’électrodes, a été développé, optimisé et évalué auprès de 25 participants. Les premiers résultats mettent en évidence une performance médiane de 83 % (score F1) pour la détection des pics ECG. Par ailleurs, une collecte de données multimodales, couvrant 75 heures de conduite simulée, a permis d’étudier les différences entre les états d’éveil et de somnolence. Les performances de classification des états montrent que l’ECG capacitif atteint un score F1 de 69,7 %, contre 86 % pour l’ECG médical. L’intégration des données physiologiques et véhiculaires améliore toutefois ces résultats, avec des scores atteignant 78.2 % pour l’ECG capacitif et 88.6 % pour l’ECG médical. Ces résultats soulignent le potentiel de l’ECG capacitif pour détecter la somnolence tout en mettant en lumière les défis liés à son intégration industrielle. Les meilleures performances ont été obtenues avec de petites électrodes positionnées au milieu du dos. Ceci dit, le système multicapteur ne semblait pas redondant : les capteurs avaient des périodes différentes d’optimalité du signal. Ceci suggère qu’un système combinant une grille de petites électrodes et la fusion de capteurs pourrait renforcer la robustesse de cette technologie. Cette approche ouvre des perspectives prometteuses pour le développement de systèmes de sécurité embarqués non invasifs, venant compléter les solutions existantes et renforcer la prévention des accidents liés à la fatigue

gargammel:a sequence simulator for ancient DNA

SUMMARY : Ancient DNA has emerged as a remarkable tool to infer the history of extinct species and past populations. However, many of its characteristics, such as extensive fragmentation, damage and contamination, can influence downstream analyses. To help investigators measure how these could impact their analyses in silico , we have developed gargammel, a package that simulates ancient DNA fragments given a set of known reference genomes. Our package simulates the entire molecular process from post-mortem DNA fragmentation and DNA damage to experimental sequencing errors, and reproduces most common bias observed in ancient DNA datasets. AVAILABILITY AND IMPLEMENTATION : The package is publicly available on github: https://grenaud.github.io/gargammel/ and released under the GPL. CONTACT : [email protected]. SUPPLEMENTARY INFORMATION : Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press

Joint Estimates of Heterozygosity and Runs of Homozygosity for Modern and Ancient Samples

Both the total amount and the distribution of heterozygous sites within individual genomes are informative about the genetic diversity of the population they belong to. Detecting true heterozygous sites in ancient genomes is complicated by the generally limited coverage achieved and the presence of post-mortem damage inflating sequencing errors. Additionally, large runs of homozygosity found in the genomes of particularly inbred individuals and of domestic animals can skew estimates of genome-wide heterozygosity rates. Current computational tools aimed at estimating runs of homozygosity and genome-wide heterozygosity levels are generally sensitive to such limitations. Here, we introduce ROHan, a probabilistic method which substantially improves the estimate of heterozygosity rates both genome-wide and for genomic local windows. It combines a local Bayesian model and a Hidden Markov Model at the genome-wide level and can work both on modern and ancient samples. We show that our algorithm outperforms currently available methods for predicting heterozygosity rates for ancient samples. Specifically, ROHan can delineate large runs of homozygosity (at megabase scales) and produce a reliable confidence interval for the genome-wide rate of heterozygosity outside of such regions from modern genomes with a depth of coverage as low as 5-6× and down to 7-8× for ancient samples showing moderate DNA damage. We apply ROHan to a series of modern and ancient genomes previously published and revise available estimates of heterozygosity for humans, chimpanzees and horses.</p