De novo finished 2.8 Mbp Staphylococcus aureus genome assembly from 100 bp short and long range paired-end reads

Motivation: Paired-end sequencing allows circumventing the shortness of the reads produced by second generation sequencers and is essential for de novo assembly of genomes. However, obtaining a finished genome from short reads is still an open challenge. We present an algorithm that exploits the pairing information issued from inserts of potentially any length. The method determines paths through an overlaps graph by using a constrained search tree. We also present a method that automatically determines suited overlaps cutoffs according to the contextual coverage, reducing thus the need for manual parameterization. Finally, we introduce an interactive mode that allows querying an assembly at targeted regions. Results: We assess our methods by assembling two Staphylococcus aureus strains that were sequenced on the Illumina platform. Using 100 bp paired-end reads and minimal manual curation, we produce a finished genome sequence for the previously undescribed isolate SGH-10-168. Availability and implementation: The presented algorithms are implemented in the standalone Edena software, freely available under the General Public License (GPLv3) at www.genomic.ch/edena.php. Contact: [email protected] Supplementary Information: Supplementary data are available at Bioinformatics onlin

Ornithological observations in Senegal

Ornithological observations in Senegal. We present observations made in Senegal in January 2015. Five sightings of rare species are described: a White-crested Tiger Heron Tigriornis leucolopha in the Saloum delta, a Shorteared Owl Asio flammeus in Madeleine Islands National Park, an Egyptian Nightjar Caprimulgus aegyptius in Djoudj National Park, a Shining-blue Kingfisher Alcedo quadribrachys in Niokolo-Koba National Park, and a Greater Hoopoe Lark Alaemon alaudipes in the Ndiael reserve. The predation of a Cattle Egret Bubulcus ibis by a Martial Eagle Polemaetus bellicosus, and the life history of a ringed Black-tailed Godwit Limosa limosa, are presented

Foisonnement de l'innovation agricole : quelques exemples d'initiatives en élevage herbivore

Les témoignages rassemblés pour illustrer le foisonnement des innovations agricoles émanent d'acteurs différents (agriculteurs, recherche, développement) mais sont tous caractérisés par des approches plutôt systémiques et des dynamiques de co-conception. Les thèmes abordés concernent la production (valorisation des surfaces avec des cultures dérobées, sélection d'espèce prairiales locales), l'appropriation de résultats de recherche (amélioration de la gestion des prairies), la conception d'itinéraires techniques (solutions pour limiter les pertes d'azote en rotation prairie - prairie), l'évaluation de systèmes (repérer des pratiques innovantes en mobilisant des principes de l'agroécologie) mais aussi l'amélioration des conditions de travail et la formation (communication « intergénérationnelle » entre des paysans herbagers et des élèves)

Relationship between QT interval and outcome in low-flow low-gradient aortic stenosis with low left ventricular ejection fraction

Background QT interval has been shown to be associated with cardiovascular events. There is no data regarding the association between QT interval and left ventricular (LV) function and prognosis in patients with low LV ejection fraction (LVEF), low‐flow, low‐gradient aortic stenosis (LF‐LG AS). We aimed to examine the relationship between corrected QT interval (QT c) and LV function and outcome in these patients. Methods and Results Ninety‐three patients (73±10 years; 74% men) with LF‐LG AS (mean gradient 450 ms in men and >470 ms in women. LV global longitudinal strain was measured by speckle tracking and expressed in absolute value |%|. QT c correlated with the following: global longitudinal strain (r=−0.40, P=0.005), LVEF (r=−0.27, P=0.02), stroke volume (r=−0.35, P=0.007), and B‐type natriuretic peptide (r=0.45, P=0.0006). During a median follow‐up of 2.0 years, 49 patients died. Prolonged QT c was associated with a 2‐fold increase in all‐cause mortality (hazard ratio=2.05; P=0.01) and cardiovascular mortality (hazard ratio=1.89; P=0.04). In multivariable analysis adjusted for EuroSCORE, aortic valve replacement, previous myocardial infarction, LVEF, and ß‐blocker medication, prolonged QT c was independently associated with all‐cause mortality (hazard ratio=2.56; P=0.008) and cardiovascular mortality (hazard ratio=2.50; P=0.02). Conclusions In patients with LF‐LG AS and reduced LVEF, longer QT c interval was associated with worse LV function and increased risk of death. Assessment of QT c may provide a simple and inexpensive tool to enhance risk stratification in LF‐LG AS patients

Semi-empirical dissipation source functions for ocean waves: Part I, definition, calibration and validation

New parameterizations for the spectra dissipation of wind-generated waves are proposed. The rates of dissipation have no predetermined spectral shapes and are functions of the wave spectrum and wind speed and direction, in a way consistent with observation of wave breaking and swell dissipation properties. Namely, the swell dissipation is nonlinear and proportional to the swell steepness, and dissipation due to wave breaking is non-zero only when a non-dimensional spectrum exceeds the threshold at which waves are observed to start breaking. An additional source of short wave dissipation due to long wave breaking is introduced to represent the dissipation of short waves due to longer breaking waves. Several degrees of freedom are introduced in the wave breaking and the wind-wave generation term of Janssen (J. Phys. Oceanogr. 1991). These parameterizations are combined and calibrated with the Discrete Interaction Approximation of Hasselmann et al. (J. Phys. Oceangr. 1985) for the nonlinear interactions. Parameters are adjusted to reproduce observed shapes of directional wave spectra, and the variability of spectral moments with wind speed and wave height. The wave energy balance is verified in a wide range of conditions and scales, from gentle swells to major hurricanes, from the global ocean to coastal settings. Wave height, peak and mean periods, and spectral data are validated using in situ and remote sensing data. Some systematic defects are still present, but the parameterizations yield the best overall results to date. Perspectives for further improvement are also given.Comment: revised version for Journal of Physical Oceanograph

Awakening the control of the ankle dorsiflexors in the post-stroke hemiplegic subject to improve walking activity and social participation: the WAKE (Walking Ankle isoKinetic Exercise) randomised, controlled trial

Stroke is the leading cause of acquired disability in France. While 90% of patients recover the ability to walk, it is often limited with a steady speed of approximately 0.7 m/s. This limitation of walking activity is partly related to a decrease in strength associated with more or less significant spasticity. In particular, it seems that the strength of the dorsiflexor muscles is directly related to walking speed. We hypothesise that a protocol based on gestural repetition targeted at the ankle during the subacute phase potentiates the recovery of motor control, improving walking activity, and participates in recovering better social participation