Impact of PGPR inoculation on root morphological traits and root exudation in rapeseed and camelina: interactions with heat stress.

Root exudation is involved in the recruitment of beneficial microorganisms by trophic relationships and/or signalling pathways. Among beneficial microorganisms, Plant Growth-Promoting Rhizobacteria (PGPR) are known to improve plant growth and stress resistance. These interactions are of particular importance for species that do not interact with mycorrhizal fungi, such as rapeseed (Brassica napus L.) and camelina (Camelina sativa (L.) Crantz). However, heat stress is known to have a quantitative and qualitative impact on root exudation and could affect the interactions between plants and PGPR. We aimed to analyse the effects of PGPR inoculation on root morphology and exudation in rapeseed and camelina at the reproductive stage. The modulation of the effects of these interactions under heat stress was also investigated. The plants were inoculated twice at the reproductive stage with two different Pseudomonas species and were exposed to heat stress after the second inoculation. In non-stressing conditions, after bacterial inoculation, rapeseed and camelina exhibited two contrasting behaviours in C root allocation. While rapeseed plants seemed to suffer from the interactions with the bacteria, camelina plants appeared to control the relationship with the PGPR by modifying the composition of their root exudates. Under heat stress, the plant-PGPR interaction was unbalanced for rapeseed, for which the C allocation strategy is mainly driven by the C cost from the bacteria. Alternatively, camelina plants prioritized C allocation for their own above-ground development. This work opens up new perspectives for understanding plant-PGPR interactions, especially in an abiotic stress context.

ConvSCCS: convolutional self-controlled case series model for lagged adverse event detection.

With the increased availability of large electronic health records databases comes the chance of enhancing health risks screening. Most post-marketing detection of adverse drug reaction (ADR) relies on physicians' spontaneous reports, leading to under-reporting. To take up this challenge, we develop a scalable model to estimate the effect of multiple longitudinal features (drug exposures) on a rare longitudinal outcome. Our procedure is based on a conditional Poisson regression model also known as self-controlled case series (SCCS). To overcome the need of precise risk periods specification, we model the intensity of outcomes using a convolution between exposures and step functions, which are penalized using a combination of group-Lasso and total-variation. Up to our knowledge, this is the first SCCS model with flexible intensity able to handle multiple longitudinal features in a single model. We show that this approach improves the state-of-the-art in terms of mean absolute error and computation time for the estimation of relative risks on simulated data. We apply this method on an ADR detection problem, using a cohort of diabetic patients extracted from the large French national health insurance database (SNIIRAM), a claims database containing medical reimbursements of more than 53 million people. This work has been done in the context of a research partnership between Ecole Polytechnique and CNAMTS (in charge of SNIIRAM).

Burden of fractures in France: incidence and severity by age, gender, and site in 2016.

PURPOSE: Fractures are common events, but the exact incidence and severity of fractures have not been clearly determined for most anatomical sites. We estimated the incidence and severity of fractures in France regardless of the anatomical site. METHODS: Observational cross-sectional study in France in 2016 based on the national health data system. All incident fractures in patients 20 years and older were included. We determined the anatomical fracture site (12 sites) and the severity using a 4-point scale (outpatient care, hospitalization, surgery, and in-hospital death). RESULTS: We identified 562,094 incident fractures, predominantly occurring in women (319,858: 56.9%); with a mean age of 63.6 years, and an exponential increase after the age of 70 years. Distal upper limb (172,591: 30.7%), distal lower limb (84,602: 15.1%), and femoral neck (78,766: 14.0%) accounted for more than one-half of all fractures. Sex and age of onset distributions varied widely according to fracture sites, with earlier onset for distal lower limb fractures (mean age: 54.2 years) and distal upper limb fractures (mean age: 55.2 years) with a men predominance for skull fractures. Only 105,165 (18.7%) fractures were treated on an outpatient basis; 11,913 (2.1%) in-hospital deaths occurred in patients with a mean age of 79.5 years. High mortality was observed for skull (12.9%), rib (4.9%), and femoral fractures (femoral neck 4.3% and proximal lower limb 4.2%). CONCLUSION: We estimated the incidence of fractures in France by sex and anatomical site. We also showed that fractures remain common and serious life events, especially in older people.

Estimating time-to-onset of adverse drug reactions from spontaneous reporting databases.

BACKGROUND: Analyzing time-to-onset of adverse drug reactions from treatment exposure contributes to meeting pharmacovigilance objectives, i.e. identification and prevention. Post-marketing data are available from reporting systems. Times-to-onset from such databases are right-truncated because some patients who were exposed to the drug and who will eventually develop the adverse drug reaction may do it after the time of analysis and thus are not included in the data. Acknowledgment of the developments adapted to right-truncated data is not widespread and these methods have never been used in pharmacovigilance. We assess the use of appropriate methods as well as the consequences of not taking right truncation into account (naive approach) on parametric maximum likelihood estimation of time-to-onset distribution. METHODS: Both approaches, naive or taking right truncation into account, were compared with a simulation study. We used twelve scenarios for the exponential distribution and twenty-four for the Weibull and log-logistic distributions. These scenarios are defined by a set of parameters: the parameters of the time-to-onset distribution, the probability of this distribution falling within an observable values interval and the sample size. An application to reported lymphoma after anti TNF- α treatment from the French pharmacovigilance is presented. RESULTS: The simulation study shows that the bias and the mean squared error might in some instances be unacceptably large when right truncation is not considered while the truncation-based estimator shows always better and often satisfactory performances and the gap may be large. For the real dataset, the estimated expected time-to-onset leads to a minimum difference of 58 weeks between both approaches, which is not negligible. This difference is obtained for the Weibull model, under which the estimated probability of this distribution falling within an observable values interval is not far from 1. CONCLUSIONS: It is necessary to take right truncation into account for estimating time-to-onset of adverse drug reactions from spontaneous reporting databases.

A new, sensitive marine microalgal recombinant biosensor using luminescence monitoring for toxicity testing of antifouling biocides.

In this study, we propose the use of the marine green alga Ostreococcus tauri, the smallest free-living eukaryotic cell known to date, as a new luminescent biosensor for toxicity testing in the environment. Diuron and Irgarol 1051, two antifouling biocides commonly encountered in coastal waters, were chosen to test this new biosensor along with two degradation products of diuron. The effects of various concentrations of the antifoulants on four genetic constructs of O. tauri (based on genes involved in photosynthesis, cell cycle, and circadian clock) were compared using 96-well culture microplates and a luminometer to automatically measure luminescence over 3 days. This was compared to growth inhibition of O. tauri wild type under the same conditions. Luminescence appeared to be more sensitive than growth inhibition as an indicator of toxicity. Cyclin-dependent kinase (CDKA), a protein involved in the cell cycle, fused to luciferase (CDKA-Luc) was found to be the most sensitive of the biosensors, allowing an accurate determination of the 50% effective concentration (EC(50)) after only 2 days (diuron, 5.65 ± 0.44 µg/liter; Irgarol 1015, 0.76 ± 0.10 µg/liter). The effects of the antifoulants on the CDKA-Luc biosensor were then compared to growth inhibition in natural marine phytoplankton. The effective concentrations of diuron and Irgarol 1051 were found to be similar, indicating that this biosensor would be suitable as a reliable ecotoxicological test. The advantage of this biosensor over cell growth inhibition testing is that the process can be easily automated and could provide a high-throughput laboratory approach to perform short-term toxicity tests. The ability to genetically transform and culture recombinant O. tauri gives it huge potential for screening many other toxic compounds.

Silicon Supply Improves Nodulation and Dinitrogen Fixation and Promotes Growth in Trifolium incarnatum Subjected to a Long-Term Sulfur Deprivation.

In many crops species, sulfur (S) deprivation negatively affects growth, seed yield quality and plant health. Furthermore, silicon (Si) is known to alleviate many nutritional stresses but the effects of Si supply on plants subjected to S deficiency remain unclear and poorly documented. The objective of this study was to evaluate whether Si supply would alleviate the negative effects of S deprivation on root nodulation and atmospheric dinitrogen (N2) fixation capacity in Trifolium incarnatum subjected (or not) to long-term S deficiency. For this, plants were grown for 63 days in hydroponic conditions with (500 µM) or without S and supplied (1.7 mM) or not with Si. The effects of Si on growth, root nodulation and N2 fixation and nitrogenase abundance in nodules have been measured. The most important beneficial effect of Si was observed after 63 days. Indeed, at this harvest time, a Si supply increased growth, the nitrogenase abundance in nodules and N2 fixation in S-fed and S-deprived plants while a beneficial effect on the number and total biomass of nodules was only observed in S-deprived plants. This study shows clearly for the first time that a Si supply alleviates negative effects of S deprivation in Trifolium incarnatum.

Memory or acclimation of water stress in pea rely on root system's plasticity and plant's ionome modulation.

Introduction: Peas, as legume crops, could play a major role in the future of food security in the context of worldwide human nutrient deficiencies coupled with the growing need to reduce consumption of animal products. However, pea yields, in terms of quantity and quality (i.e. grain content), are both susceptible to climate change, and more specifically to water deficits, which nowadays occur more frequently during crop growth cycles and tend to last longer. The impact of soil water stress on plant development and plant growth is complex, as its impact varies depending on soil water availability (through the modulation of elements available in the soil), and by the plant's ability to acclimate to continuous stress or to memorize previous stress events. Method: To identify the strategies underlying these plant responses to water stress events, pea plants were grown in controlled conditions under optimal water treatment and different types of water stress; transient (during vegetative or reproductive periods), recurrent, and continuous (throughout the plant growth cycle). Traits related to water, carbon, and ionome uptake and uses were measured and allowed the identification typical plant strategies to cope with water stress. Conclusion: Our results highlighted (i) the common responses to the three types of water stress in shoots, involving manganese (Mn) in particular, (ii) the potential implications of boron (B) for root architecture modification under continuous stress, and (iii) the establishment of an "ecophysiological imprint" in the root system via an increase in nodule numbers during the recovery period.

SCALPEL3: A scalable open-source library for healthcare claims databases.

OBJECTIVE: This article introduces SCALPEL3 (Scalable Pipeline for Health Data), a scalable open-source framework for studies involving Large Observational Databases (LODs). It focuses on scalable medical concept extraction, easy interactive analysis, and helpers for data flow analysis to accelerate studies performed on LODs. MATERIALS AND METHODS: Inspired from web analytics, SCALPEL3 relies on distributed computing, data denormalization and columnar storage. It was compared to the existing SAS-Oracle SNDS infrastructure by performing several queries on a dataset containing a three years-long history of healthcare claims of 13.7 million patients. RESULTS AND DISCUSSION: SCALPEL3 horizontal scalability allows handling large tasks quicker than the existing infrastructure while it has comparable performance when using only a few executors. SCALPEL3 provides a sharp interactive control of data processing through legible code, which helps to build studies with full reproducibility, leading to improved maintainability and audit of studies performed on LODs. CONCLUSION: SCALPEL3 makes studies based on SNDS much easier and more scalable than the existing framework [1]. It is now used at the agency collecting SNDS data, at the French Ministry of Health and soon at the National Health Data Hub in France [2].

Impact of Bacterial Siderophores on Iron Status and Ionome in Pea.

Including more grain legumes in cropping systems is important for the development of agroecological practices and the diversification of protein sources for human and animal consumption. Grain legume yield and quality is impacted by abiotic stresses resulting from fluctuating availabilities in essential nutrients such as iron deficiency chlorosis (IDC). Promoting plant iron nutrition could mitigate IDC that currently impedes legume cultivation in calcareous soils, and increase the iron content of legume seeds and its bioavailability. There is growing evidence that plant microbiota contribute to plant iron nutrition and might account for variations in the sensitivity of pea cultivars to iron deficiency and in fine to seed nutritional quality. Pyoverdine (pvd) siderophores synthesized by pseudomonads have been shown to promote iron nutrition in various plant species (Arabidopsis, clover and grasses). This study aimed to investigate the impact of three distinct ferripyoverdines (Fe-pvds) on iron status and the ionome of two pea cultivars (cv.) differing in their tolerance to IDC, (cv. S) being susceptible and (cv. T) tolerant. One pvd came from a pseudomonad strain isolated from the rhizosphere of cv. T (pvd1T), one from cv. S (pvd2S), and the third from a reference strain C7R12 (pvdC7R12). The results indicated that Fe-pvds differently impacted pea iron status and ionome, and that this impact varied both according to the pvd and the cultivar. Plant iron concentration was more increased by Fe-pvds in cv. T than in cv. S. Iron allocation within the plant was impacted by Fe-pvds in cv. T. Furthermore, Fe-pvds had the greatest favorable impact on iron nutrition in the cultivar from which the producing strain originated. This study evidences the impact of bacterial siderophores on pea iron status and pea ionome composition, and shows that this impact varies with the siderophore and host-plant cultivar, thereby emphasizing the specificity of these plant-microorganisms interactions. Our results support the possible contribution of pyoverdine-producing pseudomonads to differences in tolerance to IDC between pea cultivars. Indeed, the tolerant cv. T, as compared to the susceptible cv. S, benefited from bacterial siderophores for its iron nutrition to a greater extent.

[Transfusion-transmitted virus (TTV) and renal failure]. / Le virus transmis par la transfusion (TTV) et insuffisance rénale.

In 1997, a new DNA virus, designated TTV "Transfusion Transmitted Virus", was isolated and seemed to be associated with non A-G post-transfusion hepatitis. The virus infects mainly patients at risk for parenteral exposure and hence, prone to develop chronic liver disease, as well as healthy populations worldwide. Few reports, however, have been published on the epidemiology and potential significance of TTV infection in patients with renal disease. This paper reviews, characterization of the virus, the history of its discovery, taxonomy and identification. Current status of TTV infection in patients with renal diseases are also summarised.

Seasonal variations in maternal provisioning of Crepidula fornicata (Gastropoda): fatty acid composition of females, embryos and larvae.

Recruitment success of marine invertebrate populations not only depends on the number of recruits but also on their quality which affects their survival. In species characterized by a mixed development (encapsulated embryonic development and release of planktotrophic larvae), the offspring quality depends on both maternal provisioning and larval feeding. Here, we investigated potential changes of maternal provisioning over the whole reproductive period in a gastropod with a mixed development: Crepidula fornicata. In its introduction area, C. fornicata reproduces from February to October, which implies that both adults and larvae are exposed to different food availabilities. Maternal provisioning was assessed by measuring the fatty acid (FA) composition of females, encapsulated embryos and larvae, in February, May, July and September 2009. FA are essential resources for the development of embryos and larvae, and are key biomarkers of offspring quality. Our results showed differences in FA composition between muscles, visceral masses, and encapsulated embryos. In particular, FA composition of embryos was similar to that of the visceral mass. Seasonal variations in FA composition were observed: in the middle of the reproductive season (May and July), female tissues and embryos showed a higher proportion of polyunsaturated fatty acids and especially ω3, as compared to the beginning and end of the reproductive season (February and September). This showed that through maternal provisioning the quality of C. fornicata offspring was higher in the middle of the reproductive season. Whether this would result in an increase of recruitment success and juvenile performance would require further investigations.