miRkwood: a tool for the reliable identification of microRNAs in plant genomes

International audienceBackground: MicroRNAs (miRNAs) play crucial roles in post-transcriptional regulation of eukaryotic gene expression and are involved in many aspects of plant development. Although several prediction tools are available for metazoan genomes, the number of tools dedicated to plants is relatively limited. Results: Here, we present miRkwood, a user-friendly tool for the identification of miRNAs in plant genomes using small RNA sequencing data. Deep-sequencing data of Argonaute associated small RNAs showed that miRkwood is able to identify a large diversity of plant miRNAs and limits false positive predictions. Moreover, it outperforms current tools such as ShortStack and contrary to ShortStack, miRkwood provides a quality score allowing users to rank miRNA predictions. Conclusion: miRkwood is a very efficient tool for the annotation of miRNAs in plant genomes. It is available as a web server, as a standalone version, as a docker image and as a Galaxy tool

Impact of Zika Virus Emergence in French Guiana: A Large General Population Seroprevalence Survey.

BACKGROUND: Since the identification of Zika virus (ZIKV) in Brazil in May 2015, the virus has spread throughout the Americas. However, ZIKV burden in the general population in affected countries remains unknown. METHODS: We conducted a general population survey in the different communities of French Guiana through individual interviews and serologic survey during June-October 2017. All serum samples were tested for anti-ZIKV immunoglobulin G antibodies using a recombinant antigen-based SGERPAxMap microsphere immunoassay, and some of them were further evaluated through anti-ZIKV microneutralization tests. RESULTS: The overall seroprevalence was estimated at 23.3% (95% confidence interval [CI], 20.9%-25.9%) among 2697 participants, varying from 0% to 45.6% according to municipalities. ZIKV circulated in a large majority of French Guiana but not in the most isolated forest areas. The proportion of reported symptomatic Zika infection was estimated at 25.5% (95% CI, 20.3%-31.4%) in individuals who tested positive for ZIKV. CONCLUSIONS: This study described a large-scale representative ZIKV seroprevalence study in South America from the recent 2015-2016 Zika epidemic. Our findings reveal that the majority of the population remains susceptible to ZIKV, which could potentially allow future reintroductions of the virus

A value-based comparison of the management of ambulatory respiratory diseases in walk-in clinics, primary care practices, and emergency departments : protocol for a multicenter prospective cohort study

Background: In Canada, 30%-60% of patients presenting to emergency departments are ambulatory. This category has been labeled as a source of emergency department overuse. Acting on the presumption that primary care practices and walk-in clinics offer equivalent care at a lower cost, governments have invested massively in improving access to these alternative settings in the hope that patients would present there instead when possible, thereby reducing the load on emergency departments. Data in support of this approach remain scarce and equivocal. Objective: The aim of this study is to compare the value of care received in emergency departments, walk-in clinics, and primary care practices by ambulatory patients with upper respiratory tract infection, sinusitis, otitis media, tonsillitis, pharyngitis, bronchitis, influenza-like illness, pneumonia, acute asthma, or acute exacerbation of chronic obstructive pulmonary disease. Methods: A multicenter prospective cohort study will be performed in Ontario and Québec. In phase 1, a time-driven activity-based costing method will be applied at each of the 15 study sites. This method uses time as a cost driver to allocate direct costs (eg, medication), consumable expenditures (eg, needles), overhead costs (eg, building maintenance), and physician charges to patient care. Thus, the cost of a care episode will be proportional to the time spent receiving the care. At the end of this phase, a list of care process costs will be generated and used to calculate the cost of each consultation during phase 2, in which a prospective cohort of patients will be monitored to compare the care received in each setting. Patients aged 18 years and older, ambulatory throughout the care episode, and discharged to home with one of the aforementioned targeted diagnoses will be considered. The estimated sample size is 1485 patients. The 3 types of care settings will be compared on the basis of primary outcomes in terms of the proportion of return visits to any site 3 and 7 days after the initial visit and the mean cost of care. The secondary outcomes measured will include scores on patient-reported outcome and experience measures and mean costs borne wholly by patients. We will use multilevel generalized linear models to compare the care settings and an overlap weights approach to adjust for confounding factors related to age, sex, gender, ethnicity, comorbidities, registration with a family physician, socioeconomic status, and severity of illness. Results: Phase 1 will begin in 2021 and phase 2, in 2023. The results will be available in 2025. Conclusions: The end point of our program will be for deciders, patients, and care providers to be able to determine the most appropriate care setting for the management of ambulatory emergency respiratory conditions, based on the quality and cost of care associated with each alternative

Assessing the Effects of Periodic Flooding on the Population Structure and Recruitment Rates of Riparian Tree Forests

Riparian forest stands are subjected to a variety of hydrological stresses as a result of annual fluctuations in water levels during the growing season. Spring floods create additional water-related stress as a result of a major inflow of water that floods riverside land. This exploratory study assesses the impacts of successive floods on tree dynamics and regeneration in an active sedimentation area, while determining the age of the stands using the recruitment rates, tree structure and tree rings based on dendrochronological analysis. Environmental data were also recorded for each vegetation quadrat. In total, 2633 tree stems were tallied throughout the quadrats (200 m2), and tree specimens were analyzed based on the various flood zones. A total of 720 specimens were counted (100 m2 strip) to measure natural regeneration. Higher recruitment rates are noted for the no-flood zones and lower rates in active floodplains. During the period of the establishment of tree species, the survival rates are comparable between the flood zones and the no-flood zones. Tree diameter distribution reveals a strong predominance of young trees in flooded areas. Different factors appear to come into play in the dynamics of riparian forest stands, including the disruptions associated with successive flooding

A Comparison of the Composition and Diversity of Tree Populations along a Hydrological Gradient in Floodplains (Southern Québec, Canada)

With the current climate changes, it is essential to understand the mechanisms that govern floods and flow regimes and their effects on the dynamics of riparian forests. The aim is to assess the effects of new hydrological conditions (increase in flood frequency) on forest stands subject to frequent floods. The sampling sites (total of 94 quadrats) are located in riverine woodlands, and the choice of location corresponds to the boundaries of the flood-risk zones established by official government maps. Our study shows that there are significant differences in the composition and diversity of forest communities following differences in the flood recurrence zones. In the active floodplains (i.e., recurrence interval of 0–20 years), the tree population stands are clearly distinguished from other intermediate flood zones (interval of 20–100 years). Differences are also noted in the structure of the communities, in particular in the frequent flood zones, which are characterized by a low renewal rate, low density and less-diversified forest stands. The frequent floods risk forest stand rejuvenation and creating decline as a result of increased tree mortality and the low renewal rate. With the expected increases in the number of flood events in the coming decades, there may be greater tree mortality and a gradual disappearance of the forest communities

Characterization of the Thermal Dependence of SAW Stress Sensitivity

National audienceSurface Acoustic Waves (SAW) sensors have received an increasing interest as they reveal capable to be interrogated wirelessly without on-board power supply. Their used as stress sensor allows for remarkable linearity and repeatability. SAW devices can particularly be implemented for in-plane-stress measurement, yielding temperature compensated highly sensitive and linear sensors specially when built on AT-cut quartz wafers. However, their stress sensitivity is affected by temperature and an accurate account of the thermal impact on their mechanical properties is required for designing and calibrating the sensors properly. In this paper, we propose an experimental set-up enabling one to reliably apply controlled stress conditions to quartz substrate on which SAW resonators have been built. Finally, experimental evidence of the cross relation between temperature and stress sensitivity of the resonance frequency is reported

Alloying electrode coatings towards better magnesium batteries

International audienceMastering the metal-electrolyte interface is mandatory for the development of reliable rechargeable magnesium batteries. Nevertheless, most of the current electrolytes contain chlorides species to bypass the surface passivation of magnesium, making them corrosive to other cell components and potentially irrelevant for industrial application. Here, we demonstrate a novel approach to bypass the use of such electrolytes via the mediation of an alloy-type interface prepared by coating the surface of a magnesium electrode with liquid gallium. The chemical alloying induces the formation of a surface layer, mainly composed of the intermetallic Mg2Ga5, enabling significantly improved electrochemical performance with a simple chloride-free Mg(TFSI)2/DME electrolyte. Sensibly less-polarized and more stable plating/stripping is observed with symmetric cells, and longer cycle life is achieved in full cells with positive electrodes based on sulphur- and organic composites. This alloy-based surface protection opens the door to electrolytes firstly considered as non-compatible with magnesium metal, and consequently paves the way to the application of metal electrodes in practical magnesium batteries