The Virtual Workshop OpenWinD : a Python Toolbox Assisting Wind Instrument Makers

International audienceOur project develops the software OpenWInD for wind instrument making. A first feature is the prediction of the acoustical response of the instrument from the knowledge of its shape (bore and holes). This can be done in the harmonic (impedance computation) and temporal (sound computation) domains. It can account for various physical situations (non constant temperature, coupling with an embouchure, ...). Discretization is done in space with 1D spectral finite elements and in time with energy consistent finite differences. The second feature is the reconstruction of the shape of an instrument that fulfils a certain objective. This can be used for bore reconstruction, and instrument design. The latter is based on a strong interaction with makers and musicians, aiming at defining interesting design parameters and objective criteria, from their point of view. After a quantitative transcription of these criteria, under the form of a cost function and a design parameter space, we implement various gradient-based optimization techniques. More precisely, we exploit the fact that the sound waves inside the instruments are solution to acoustic equations in pipes, which gives us access to the Full Waveform Inversion technique (FWI) where the gradient is characterized as the solution to another wave equation. The computational framework is flexible (in terms of models, formulations, coupling terms, objective functions...) and offers the possibility to modify the criterion by the user. The goal is to proceed iteratively between the instrument makers and the numerical optimisation tool (OpenWInD) in order to achieve, finally, criteria that are representative for the makers. In the presentation, we will demonstrate and discuss some comparisons between measurements and simulation on real instruments

Axo-axonic cells in neuropsychiatric disorders: a systematic review

Imbalance between excitation and inhibition in the cerebral cortex is one of the main theories in neuropsychiatric disorder pathophysiology. Cortical inhibition is finely regulated by a variety of highly specialized GABAergic interneuron types, which are thought to organize neural network activities. Among interneurons, axo-axonic cells are unique in making synapses with the axon initial segment of pyramidal neurons. Alterations of axo-axonic cells have been proposed to be implicated in disorders including epilepsy, schizophrenia and autism spectrum disorder. However, evidence for the alteration of axo-axonic cells in disease has only been examined in narrative reviews. By performing a systematic review of studies investigating axo-axonic cells and axo-axonic communication in epilepsy, schizophrenia and autism spectrum disorder, we outline convergent findings and discrepancies in the literature. Overall, the implication of axo-axonic cells in neuropsychiatric disorders might have been overstated. Additional work is needed to assess initial, mostly indirect findings, and to unravel how defects in axo-axonic cells translates to cortical dysregulation and, in turn, to pathological states

L’inhibition de la transcription par la dactinomycine révèle une nouvelle caractéristique du stress cellulaire immunogène

Chemotherapy still constitutes the standard treatment for most cancers. Yet, some chemotherapeutics are able to trigger pre-mortem stress signals which activate an antitumor immune response and thereby confer long term protection. We used an established model built on artificial intelligence to identify, among a library of 50,000 compounds, anticancer agents that, based on their physicochemical characteristics, were predicted to induce immunogenic cell death (ICD). This algorithm led us to the identification of dactinomycin, which indeed activates the mechanisms preceding dendritic cell activation in vitro and demonstrates immune-dependent anticancer effects in vivo. Dactinomycin, mainly used to treat pediatric sarcomas, is known as able to inhibit transcription. We therefore investigated whether other ICD inducers would share this characteristic. Different immunogenic chemotherapeutics indeed inhibited RNA synthesis and secondarily translation, accompanied by an activation of ICD-related signaling. A retrospective in silico study revealed that agents annotated as inhibitors of RNA or protein synthesis are predicted as immunogenic. These results establish the inhibition of RNA synthesis as a major initial event for ICD induction.La chimiothérapie constitue encore le traitement de référence pour la majorité des cancers. Or certains agents chimiothérapeutiques sont capables de déclencher des signaux de stress pre-mortem permettant d’activer une réponse immunitaire antitumorale et confèrent ainsi une protection à long terme. A l'aide d'un modèle construit par intelligence artificielle, nous avons identifié, parmi une librairie comprenant 50 000 composés, des agents anti-cancéreux qui, d'après leurs propriétés physico-chimiques, pourraient induire une mort cellulaire immunogène (ICD, de l'anglais "immunogenic cell death"). Cet algorithme nous a permis d'identifier la dactinomycine, qui, en effet, active les mécanismes sous-jacents à l'activation des cellules dendritiques in vitro et a un effet anti-cancéreux dépendant du système immunitaire in vivo. La dactinomycine, utilisée en clinique pour le traitement de sarcomes pédiatriques, est connue pour sa capacité à inhiber la transcription. Nous nous sommes donc demandé si d'autres inducteurs de l'ICD partageaient cette propriété. Différentes chimiothérapies immunogènes induisent en effet une inhibition de la synthèse d’ARN, qui est suivie d'une inhibition de la traduction et s’accompagne de l’activation des différentes voies de l’ICD. De plus, une étude rétrospective in silico révèle que les agents classés comme inhibiteurs de la synthèse d’ARN ou de protéines sont prédits comme étant immunogènes. Ces résultats montrent que l’inhibition de la transcription est un évènement précurseur essentiel à l’activation d’une mort cellulaire immunogène

Autophagy induction by thiostrepton improves the efficacy of immunogenic chemotherapy

BackgroundImmunogenic cell death (ICD) is a peculiar modality of cellular demise that elicits adaptive immune responses and triggers T cell-dependent immunity.MethodsFluorescent biosensors were employed for an unbiased drug screen approach aiming at the identification of ICD enhancers.ResultsHere, we discovered thiostrepton as an enhancer of ICD able to boost chemotherapy-induced ATP release, calreticulin exposure and high-mobility group box 1 exodus. Moreover, thiostrepton enhanced anticancer immune responses of oxaliplatin (OXA) in vivo in immunocompetent mice, yet failed to do so in immunodeficient animals. Consistently, thiostrepton combined with OXA altered the ratio of cytotoxic T lymphocytes to regulatory T cells, thus overcoming immunosuppression and reinstating anticancer immunosurveillance.ConclusionAltogether, these results indicate that thiostrepton can be advantageously combined with chemotherapy to enhance anticancer immunogenicity

EIF2α phosphorylation: a hallmark of both autophagy and immunogenic cell death

Different intrinsic and extrinsic stress pathways including endoplasmic reticulum (ER) stress converge on the phosphorylation of eukaryotic translation initiation factor 2A (EIF2A, best known as eIF2α), which characterizes the so-called “integrated stress response”. This phosphorylation event is important for the induction of autophagy in response to multiple distinct stressors, as well as for the exposure of calreticulin (CALR) as an “eat me” signal on the surface of the plasma membrane of stressed cells. Both autophagy and CALR exposure are required for immunogenic cell death, a modality of cellular demise that ignites anticancer and antiviral immune responses. In several different cancer types, eIF2α phosphorylation indicates favorable prognosis, correlating with an enhanced antitumor immune response

Full waveform inversion for bore reconstruction of woodwind-like instruments

The internal geometry of a wind instrument can be estimated from acoustic measurements. For woodwind instruments, this involves characterizing the inner shape (bore) but also the side holes (dimensions and location). In this study, the geometric parameters are recovered by a gradient-based optimization process, which minimizes the deviation between simulated and measured linear acoustic responses of the resonator for several fingerings through an observable function. The acoustic fields are computed by solving a linear system resulting from the 1D spectral finite elements spatial discretization of the wave propagation equations (including thermo-viscous effects, radiation and side holes). The “full waveform inversion” (FWI) technique exploits the fact that the gradient of the cost function can be computed by solving the same linear system as that of the direct problem but with a different source term. The gradient is computed with better accuracy and less additional cost than with finite-difference. The dependence of the cost function on the choice of the observed quantity, the frequency range and the fingerings used, is first analyzed. Then, the FWI is used to reconstruct, from measured impedances, an elementary instrument with 14 design variables. The results, obtained in about 1 minute on a laptop, are in excellent agreement with the direct geometric measurements

Trial watch: intratumoral immunotherapy

International audienceWhile chemotherapy and radiotherapy remain the first-line approaches for the management of most unresectable tumors, immunotherapy has emerged in the past two decades as a game-changing treatment, notably with the clinical success of immune checkpoint inhibitors. Immunotherapies aim at (re) activating anticancer immune responses which occur in two main steps: (1) the activation and expansion of tumor-specific T cells following cross-presentation of tumor antigens by specialized myeloid cells (priming phase); and (2) the immunological clearance of malignant cells by these antitumor T lymphocytes (effector phase). Therapeutic vaccines, adjuvants, monoclonal antibodies, cytokines, immunogenic cell death-inducing agents including oncolytic viruses, anthracycline-based chemotherapy and radiotherapy, as well as adoptive cell transfer, all act at different levels of this cascade to (re)instate cancer immunosurveillance. Intratumoral delivery of these immunotherapeutics is being tested in clinical trials to promote superior antitumor immune activity in the context of limited systemic toxicity

High-throughput label-free detection of DNA-to-RNA transcription inhibition using brightfield microscopy and deep neural networks

International audienceDrug discovery is in constant evolution and major advances have led to the development of in vitro high-throughput technologies, facilitating the rapid assessment of cellular phenotypes. One such phenotype is immunogenic cell death, which occurs partly as a consequence of inhibited RNA synthesis. Automated cell-imaging offers the possibility of combining high-throughput with high-content data acquisition through the simultaneous computation of a multitude of cellular features. Usually, such features are extracted from fluorescence images, hence requiring labeling of the cells using dyes with possible cytotoxic and phototoxic side effects. Recently, deep learning approaches have allowed the analysis of images obtained by brightfield microscopy, a technique that was for long underexploited, with the great advantage of avoiding any major interference with cellular physiology or stimulatory compounds. Here, we describe a label-free image-based high-throughput workflow that accurately detects the inhibition of DNA-to-RNA transcription. This is achieved by combining two successive deep convolutional neural networks, allowing (1) to automatically detect cellular nuclei (thus enabling monitoring of cell death) and (2) to classify the extracted nuclear images in a binary fashion. This analytical pipeline is R-based and can be easily applied to any microscopic platform

Phosphorylation of eukaryotic initiation factor-2α (eIF2α) in autophagy

International audienceThe integrated stress response is characterized by the phosphorylation of eukaryotic initiation factor-2α (eIF2α) on serine 51 by one out of four specific kinases (EIF2AK1 to 4). Here we provide three series of evidence suggesting that macroautophagy (to which we refer to as autophagy) induced by a variety of distinct pharmacological agents generally requires this phosphorylation event. First, the induction of autophagic puncta by various distinct compounds was accompanied by eIF2α phosphorylation on serine 51. Second, the modulation of autophagy by >30 chemically unrelated agents was partially inhibited in cells expressing a non-phosphorylable (S51A) mutant of eIF2α or lacking all four eIF2α kinases, although distinct kinases were involved in the response to different autophagy inducers. Third, inhibition of eIF2α phosphatases was sufficient to stimulate autophagy. In synthesis, it appears that eIF2α phosphorylation is a central event for the stimulation of autophagy

Calcium signaling and cell cycle: Progression or death

Cytosolic Ca2+ concentration levels fluctuate in an ordered manner along the cell cycle, in line with the fact that Ca2+ is involved in the regulation of cell proliferation. Cell proliferation should be an error-free process, yet is endangered by mistakes. In fact, a complex network of proteins ensures that cell cycle does not progress until the previous phase has been successfully completed. Occasionally, errors occur during the cell cycle leading to cell cycle arrest. If the error is severe, and the cell cycle checkpoints work perfectly, this results into cellular demise by activation of apoptotic or non-apoptotic cell death programs. Cancer is characterized by deregulated proliferation and resistance against cell death. Ca2+ is a central key to these phenomena as it modulates signaling pathways that control oncogenesis and cancer progression. Here, we discuss how Ca2+ participates in the exogenous and endogenous signals controlling cell proliferation, as well as in the mechanisms by which cells die if irreparable cell cycle damage occurs. Moreover, we summarize how Ca2+ homeostasis remodeling observed in cancer cells contributes to deregulated cell proliferation and resistance to cell death. Finally, we discuss the possibility to target specific components of Ca2+ signal pathways to obtain cytostatic or cytotoxic effects.GK is supported by the La Ligue contre le Cancer (équipe labelisée); Agence National de la Recherche (ANR) – Projets blancs; ANR under the frame of E-Rare-2, the European Research Area (ERA)-Net for Research on Rare Diseases; Association pour la recherche sur le cancer (ARC); Cancéropôle Ile-de-France; Institut National du Cancer (INCa); Institut Universitaire de France; Fondation pour la Recherche Médicale (FRM); the European Commission (ArtForce); the European Research Council (ERC); the LeDucq Foundation; the LabEx Immuno-Oncology; the RHU Torino Lumière, the SIRIC Stratified Oncology Cell DNA Repair and Tumor Immune Elimination (SOCRATE); the SIRIC Cancer Research and Personalized Medicine (CARPEM); and the Paris Alliance of Cancer Research Institutes (PACRI). LS is supported by a grant from Fondation ARC pour la recherche sur le cancer (PJA20151203519). CV and LN are supported by grants from the Ministry of Economy and Competitivity of Spain (BFU2015-70131R) and Asociación Española Contra el Cáncer (AECC). JH receives a PhD student fellowship from Fondation Philantropia.Peer reviewe