DassFlow v1.0: a variational data assimilation software for river flows

Dassflow is a computational software for river hydraulics (floods), especially designed for variational data assimilation. The forward model is based on the bidimensional shallow-water equations, solved by a finite volume method (HLLC approximate Riemann solver). It is written in Fortran 95. The adjoint code is generated by the automatic differentiation tool Tapenade. Thus, Dassflow software includes the forward solver, its adjoint code, the full optimization framework (based on the M1QN3 minimization routine) and benchmarks. The generation of new data assimilation twin experiments is easy. The software is interfaced with few pre and post-processors (mesh generators, GIS tools and visualization tools), which allows to treat real data

Variational data assimilation for 2D fluvial hydraulics simulations

International audienceA numerical method for model parameters identification is presented for a river model based on a finite volume discretization of the bidimensional shallow water equations. We use variational data assimilation to combine optimally physical information from the model and observation data of the physical system in order to identify the value of model inputs that correspond to a numerical simulation which is consistent with reality. Two numerical examples demonstrate the efficiency of the method for the identification of the inlet discharge and the bed elevation. An application to real data on the Pearl River for the identification of boundary conditions is presented

T2DInverse: Towards calibration and sensitivity analysis into Telemac2D using automatic differentiation

The industrial system Telemac2D, developed by LNHE-EDF and commercialized by Sogreah Co., is an software dedicated to the hydrodynamical and environmental modelling of maritime and river flows. It is based on finite element method and is written in Fortran 90. Our final objective is to include a full variational data assimilation process in the system. This requires the development of an adjoint model. We plan to obtain it using the Automatic Differentiation (AD) tool Tapenade v2.0. In this study, we prepare and validate a reduced version of Telemac2D that is both meant for river flows and suitable to Tapenade v2.0. Then, we establish a strategy of AD according to limitations of the current release of Tapenade (v2.0). Also, the optimization chain is achieved thanks to the unconstrained minimizer N1QN3 based on a quasi-Newton type method. The final objective is to exploit the fluvial measurements and observations in an optimal manner in Telemac2D, in order to identify the partially known or lacking parameters (bathymetry, bed friction, inflow discharge and initial state)

DassFlow v1.0: a variational data assimilation software for river flows

Dassflow is a computational software for river hydraulics (floods), especially designed for variational data assimilation. The forward model is based on the bidimensional shallow-water equations, solved by a finite volume method (HLLC approximate Riemann solver). It is written in Fortran 95. The adjoint code is generated by the automatic differentiation tool Tapenade. Thus, Dassflow software includes the forward solver, its adjoint code, the full optimization framework (based on the M1QN3 minimization routine) and benchmarks. The generation of new data assimilation twin experiments is easy. The software is interfaced with few pre and post-processors (mesh generators, GIS tools and visualization tools), which allows to treat real data

Dassflow :a Direct and Adjoint model for 2D Shallow Water flows

The Dassflow software is designed to solve the bidimensional Shallow Water equations used for the numerical modeling of river hydraulics flows. It was written to carry out variational data assimilation experiments. Based on a finite volume discretization of the Shallow Water equations, the code is written in Fortran 90. The adjoint code necessary to compute the partial derivatives of a cost function of the state variables w.r.t. the control variables of the model was developed using the automatic differentiation tool Tapenade. We present the considered equations, the theoretical bases of variational data assimilation, the numerical scheme used for solving the equations as well as the implementation of the adjoint code. Finally, we present twin experiments of data assimilation performed with Dassflow

Variational data assimilation for 2D fluvial hydraulics simulations

International audienceA numerical method for model parameters identification is presented for a river model based on a finite volume discretization of the bidimensional shallow water equations. We use variational data assimilation to combine optimally physical information from the model and observation data of the physical system in order to identify the value of model inputs that correspond to a numerical simulation which is consistent with reality. Two numerical examples demonstrate the efficiency of the method for the identification of the inlet discharge and the bed elevation. An application to real data on the Pearl River for the identification of boundary conditions is presented

Identification of equivalent topography in an open channel flow using Lagrangian data assimilation

International audienceWe present a Lagrangian data assimilation experiment in an open channel flow above a broad-crested weir. The observations consist of trajectories of particles transported by the flow and extracted from a video film, in addition to classical water level measurements. However, the presence of vertical recirculations on both sides of the weir actually conducts to the identification of an equivalent topography corresponding to the lower limit of a surface jet. In addition, results on the identification of the Manning coefficient may allow to detect the presence of bottom recirculations

Аналіз вибіркових даних при оцінюванні наукового потенціалу і характер статистичних властивостей вербальних моделей

OBJECTIVE: To determine sensitivity and specificity of a standardized recombinant cell-based indirect immunofluorescence assay (RC-IFA) for anti-Tr antibodies in comparison to a reference procedure. METHODS: Delta/Notch-like epidermal growth factor-related receptor (DNER) was expressed in HEK293 and used as a substrate for RC-IFA. HEK293 control cells expressing CDR2/Yo and CDR2L as well as mock-transfected HEK293 cells were used as controls. Serum samples from 38 patients with anti-Tr antibodies (33 with paraneoplastic cerebellar degeneration [PCD] and Hodgkin lymphoma), 66 patients with anti-Tr-negative PCD, 53 patients with Hodgkin lymphoma without neurologic symptoms, 40 patients with rheumatic diseases, and 42 healthy blood donors were tested for anti-DNER reactivity in the RC-IFA. In addition, RC-IFA results were compared to those from a commercial tissue-based IFA using monkey cerebellum. RESULTS: Using the RC-IFA, anti-DNER was detected in all anti-Tr-positive patients but in none of the controls (sensitivity 100%, 95% confidence interval [CI] 92.8%-100%; specificity 100%, 95% CI 98.7%-100%). In comparison, anti-Tr was not detected in 4 samples with low-titer autoantibodies using the commercial tissue-based assay. Preadsorption of sera with either recombinant full-length DNER or its extracellular domain selectively abolished anti-Tr reactivity. CONCLUSION: Anti-Tr antibodies bind to the extracellular domain of DNER and can be detected by RC-IFA using HEK293 cells expressing the recombinant receptor. The new method performs better than a frequently used commercial tissue-based indirect immunofluorescence assay (IFA) in samples with low-titer antibodies. CLASSIFICATION OF EVIDENCE: This study provides Class II evidence that RC-IFA accurately detects anti-Tr as compared to conventional IFA

Updated Diagnostic Criteria for Paraneoplastic Neurologic Syndromes

The contemporary diagnosis of paraneoplastic neurologic syndromes (PNSs) requires an increasing understanding of their clinical, immunologic, and oncologic heterogeneity. The 2004 PNS criteria are partially outdated due to advances in PNS research in the last 16 years leading to the identification of new phenotypes and antibodies that have transformed the diagnostic approach to PNS. Here, we propose updated diagnostic criteria for PNS.A panel of experts developed by consensus a modified set of diagnostic PNS criteria for clinical decision making and research purposes. The panel reappraised the 2004 criteria alongside new knowledge on PNS obtained from published and unpublished data generated by the different laboratories involved in the project.The panel proposed to substitute "classical syndromes" with the term "high-risk phenotypes" for cancer and introduce the concept of "intermediate-risk phenotypes." The term "onconeural antibody" was replaced by "high risk" (>70% associated with cancer) and "intermediate risk" (30%-70% associated with cancer) antibodies. The panel classified 3 levels of evidence for PNS: definite, probable, and possible. Each level can be reached by using the PNS-Care Score, which combines clinical phenotype, antibody type, the presence or absence of cancer, and time of follow-up. With the exception of opsoclonus-myoclonus, the diagnosis of definite PNS requires the presence of high- or intermediate-risk antibodies. Specific recommendations for similar syndromes triggered by immune checkpoint inhibitors are also provided.The proposed criteria and recommendations should be used to enhance the clinical care of patients with PNS and to encourage standardization of research initiatives addressing PNS.Copyright © 2021 The Author(s). Published by Wolters Kluwer Health, Inc. on behalf of the American Academy of Neurology

Mononeuritis multiplex following immune checkpoint inhibitors in malignant pleural mesothelioma

IntroductionMononeuritis multiplex is frequently related to vasculitic neuropathy and has been reported only sporadically as an adverse event of immune checkpoint inhibitors.MethodsCase series of three patients with mononeuritis multiplex—all with mesothelioma—identified in the databases of two French clinical networks (French Reference Center for Paraneoplastic Neurological Syndromes, Lyon; OncoNeuroTox, Paris; January 2015–October 2022) set up to collect and investigate n-irAEs on a nationwide level.ResultsThree patients (male; median age 86 years; range 72–88 years) had pleural mesothelioma and received 10, 4, and 6 cycles, respectively, of first-line nivolumab plus ipilimumab combined therapy. In patient 1, the neurological symptoms involved the median nerves, and in the other two patients, there was a more diffuse distribution; the symptoms were severe (common terminology criteria for adverse events, CTCAE grade 3) in all patients. Nerve conduction studies indicated mononeuritis multiplex in all patients. Peripheral nerve biopsy demonstrated necrotizing vasculitis in patients 1 and 3 and marked IgA deposition without inflammatory lesions in patient 2. Immune checkpoint inhibitors were permanently withdrawn, and corticosteroids were administered to all patients, leading to complete symptom regression (CTCAE grade 0, patient 2) or partial improvement (CTCAE grade 2, patients 1 and 3). During steroid tapering, patient 1 experienced symptom recurrence and spreading to other nerve territories (CTCAE grade 3); he improved 3 months after rituximab and cyclophosphamide administration.DiscussionWe report the occurrence of mononeuritis multiplex, a very rare adverse event of immune checkpoint inhibitors, in the three patients with mesothelioma. Clinicians must be aware of this severe, yet treatable adverse event