Learning Interactions in Reaction Diffusion Equations by Neural Networks.

Partial differential equations are common models in biology for predicting and explaining complex behaviors. Nevertheless, deriving the equations and estimating the corresponding parameters remains challenging from data. In particular, the fine description of the interactions between species requires care for taking into account various regimes such as saturation effects. We apply a method based on neural networks to discover the underlying PDE systems, which involve fractional terms and may also contain integration terms based on observed data. Our proposed framework, called Frac-PDE-Net, adapts the PDE-Net 2.0 by adding layers that are designed to learn fractional and integration terms. The key technical challenge of this task is the identifiability issue. More precisely, one needs to identify the main terms and combine similar terms among a huge number of candidates in fractional form generated by the neural network scheme due to the division operation. In order to overcome this barrier, we set up certain assumptions according to realistic biological behavior. Additionally, we use an L2-norm based term selection criterion and the sparse regression to obtain a parsimonious model. It turns out that the method of Frac-PDE-Net is capable of recovering the main terms with accurate coefficients, allowing for effective long term prediction. We demonstrate the interest of the method on a biological PDE model proposed to study the pollen tube growth problem.

Combining eddy covariance measurements with process-based modelling to enhance understanding of carbon exchange rates of dairy pastures.

Many temperate grasslands are used for dairying, and ongoing research aims to better understand these systems in order to increase animal production and soil organic carbon (SOC) stocks. However, it is difficult to fully understand management effects on SOC because most changes are slow and difficult to distinguish from natural variability, even if changes are important over years to decades. Eddy covariance (EC) measurements can overcome this problem by continuously measuring net carbon exchange from pastures, but net balances are very sensitive to even small systematic measurement errors. Combining EC measurements with detailed process-based modelling can reduce the risks inherent in total reliance on EC measurements. Modelling can also reveal information about the underlying processes that drive observed fluxes. Here, we describe carbon exchange patterns of five paddocks situated at four different locations in New Zealand and France where EC data and detailed physiological modelling were available. The work showed that respiration by grazing animals was often only incompletely captured in EC measurements. This was most problematic when fluxes were based on gap-filling, which could have estimated incorrect fluxes during grazing periods based on observations from periods without grazing. We then aimed to extract plant physiological insights from these studies. We found appreciable carbon uptake rates even at temperatures below 0 °C. After grazing, carbon uptake was reduced for up to 2 weeks. This reduction was larger than expected from reduced leaf area after grazing, but the factors contributing to that difference have not yet been identified. Detailed physiological models can also extrapolate findings to new management regimes, environmental conditions or plant attributes. This overcomes the limitation of experimental studies, which are necessarily restricted to actual site and weather conditions allowing models to make further progress on predicting management effects on SOC.

Rituximab prescription patterns and efficacy in the induction treatment of ANCA-Associated Vasculitis in a Belgian multicenter cohort.

Introduction: The RAVE trial has revolutionized induction treatment of anti-neutrophil cytoplasmic antibodies (ANCA)-Associated Vasculitis (AAV)by demonstrating the non-inferiority of rituximab (RTX) compared with cyclophosphamide.Objectives: We studied AAV patients' characteristics, RTX prescription practices and efficacy in AAV induction treatment in four Belgian university hospitals. The patient population, selected according to the Belgian reimbursement criteria, was relatively homogeneous and comparable to the one of RAVE trial.Methods: 57 patients, receiving RTX as AAV induction therapyfrom May 2014 to June 2017 were enrolled in an observational retrospective multicenter trial involving four Belgian university hospitals. We focused on the type of AAV, ANCA specificity, prescriber's specialty, used reimbursement criteria, organ involvements, severity of the flares and finally RTX efficacy in AAV induction treatment by considering the RAVE primary (complete remission without prednisone) and secondary (complete remission with prednisone <10 mg) outcomes at 6, 12, 18 and 24 months.Results: 66.7% of the patients reached complete remission with prednisone <10 mg at 6 months, 55.3% at 12 months, 40% at 18 months and 25% at 24 months. The rates of complete remission without steroids were very low at 6, 12, 18 and 24 months. The rates of relapses were high between 18 and 24 months. Conclusions: Our results confirm those of RAVE regarding complete remission rates with prednisone <10 mg/day, in a 'real-life' cohort of patients selected according to data of RAVE trial. The high prevalence of relapses - especially after 18 months - underlines the need to optimize maintenance treatment after an induction treatment with RTX..

The trade-offs between milk production and soil organic carbon storage in dairy systems under different management and environmental factors.

A possible agricultural climate change mitigation option is to increase the amount of soil organic carbon (SOC). Conversely, some factors might lead to inadvertent losses of SOC. Here, we explore the effect of various management options and environmental changes on SOC storage and milk production of dairy pastures in New Zealand. We used CenW 4.1, a process-based ecophysiological model, to run a range of scenarios to assess the effects of changes in management options, plant properties and environmental factors on SOC and milk production. We tested the model by using 2years of observations of the exchanges of water and CO2 measured with an eddy covariance system on a dairy farm in New Zealand's Waikato region. We obtained excellent agreement between the model and observations, especially for evapotranspiration and net photosynthesis. For the scenario analysis, we found that SOC could be increased through supplying supplemental feed, increasing fertiliser application, or increasing water availability through irrigation on very dry sites, but SOC decreased again for larger increases in water availability. Soil warming strongly reduced SOC. For other changes in key properties, such as changes in soil water-holding capacity and plant root:shoot ratios, SOC changes were often negatively correlated with changes in milk production. The work showed that changes in SOC were determined by the complex interplay between (1) changes in net primary production; (2) the carbon fraction taken off-site through grazing; (3) carbon allocation within the system between labile and stabilised SOC; and (4) changes in SOC decomposition rates. There is a particularly important trade-off between carbon either being removed by grazing or remaining on site and available for SOC formation. Changes in SOC cannot be fully understood unless all four factors are considered together in an overall assessment.

Acalculous cholecystitis associated with hemorrhagic fever with renal syndrome.

Hantaviruses are responsible for various types of hemorrhagic fevers depending on the involved subtype. In Europe, Puumala virus is responsible for an epidemic nephropathy. This infection can be complicated by severe abdominal pain. A rarely reported cause of this presenting symptom is acalculous cholecystitis, which must be integrated in the clinicobiological spectrum and should not lead to a surgical sanction. Its presence seems to be correlated with the severity of the disease, whose main pathophysiological phenomenon is plasma leakage induced by a microvascular endothelial dysfunction. We report the case of a young male patient who presented with severe hantavirus infection complicated by acalculous cholecystitis.