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Extended-depth of field random illumination microscopy, EDF-RIM, provides super-resolved projective imaging
No full textInternational audienceThe ultimate aim of fluorescence microscopy is to achieve high-resolution imaging of increasingly larger biological samples. Extended depth of field presents a potential solution to accelerate imaging of large samples when compression of information along the optical axis is not detrimental to the interpretation of images. We have implemented an extended depth of field (EDF) approach in a random illumination microscope (RIM). RIM uses multiple speckled illuminations and variance data processing to double the resolution. It is particularly adapted to the imaging of thick samples as it does not require the knowledge of illumination patterns. We demonstrate highly-resolved projective images of biological tissues and cells. Compared to a sequential scan of the imaged volume with conventional 2D-RIM, EDF-RIM allows an order of magnitude improvement in speed and light dose reduction, with comparable resolution. As the axial information is lost in an EDF modality, we propose a method to retrieve the sample topography for samples that are organized in cell sheets
Real-time forecasting of COVID-19-related hospital strain in France using a non-Markovian mechanistic model
No full textInternational audienceProjects such as the European Covid-19 Forecast Hub publish forecasts on the national level for new deaths, new cases, and hospital admissions, but not direct measurements of hospital strain like critical care bed occupancy at the sub-national level, which is of particular interest to health professionals for planning purposes. We present a sub-national French framework for forecasting hospital strain based on a non-Markovian compartmental model, its associated online visualisation tool and a retrospective evaluation of the real-time forecasts it provided from January to December 2021 by comparing to three baselines derived from standard statistical forecasting methods (a naive model, auto-regression, and an ensemble of exponential smoothing and ARIMA). In terms of median absolute error for forecasting critical care unit occupancy at the two-week horizon, our model only outperformed the naive baseline for 4 out of 14 geographical units and underperformed compared to the ensemble baseline for 5 of them at the 90% confidence level ( n = 38). However, for the same level at the 4 week horizon, our model was never statistically outperformed for any unit despite outperforming the baselines 10 times spanning 7 out of 14 geographical units. This implies modest forecasting utility for longer horizons which may justify the application of non-Markovian compartmental models in the context of hospital-strain surveillance for future pandemics
Le microbiome humain : 340 ans d’histoire, 140 ans d’interrogations, d’innovations technologiques et émergence de la « médecine microbienne »
No full textInternational audienceFor 350 years, we have known that the human body hosts microbes, then called “animalcules”. For over a century, following the demonstration of the role of some of these microbes in diseases, questions have arisen about the role of the largely predominant ones colonizing human skin and mucous surfaces, particularly the rich microbial ecosystem of the intestine, the gut microbiota. From the invention of germ-free life – axenism – which experimentally validated the human-microbe symbiosis, resulting from a long coevolution, to the development of anaerobic culture methods, then to the invention of molecular diagnosis, deep sequencing opening up metagenomic and omics approaches in general, a remarkable race has taken place between technological innovations and conceptual advances. This race, beyond the exhaustive description of the microbiota in its intra- and inter-human diversity, and the essential symbiotic functions of the microbiome, has paved the way for a new field of medicine: microbial medicine.On sait depuis 340ans que le corps humain héberge des microbes, alors appelés « animalcules ». Depuis plus d’un siècle, après la démonstration de la responsabilité de certains de ces microbes dans les maladies, on s’interroge sur le rôle de ceux – largement majoritaires – qui colonisent les surfaces cutanées et muqueuses humaines, particulièrement le riche écosystème microbien de l’intestin, le microbiote intestinal. De l’invention de la vie sans germe (axénie), qui a permis de valider expérimentalement la symbiose entre êtres humains et microbes, fruit d’une longue coévolution, à la mise au point des méthodes de culture anaérobies, puis à l’invention du diagnostic moléculaire, du séquençage profond ouvrant les approches métagénomiques et omiques en général, une formidable course s’est déroulée entre innovations technologiques et avancées conceptuelles. Cette course, au-delà de la description exhaustive du microbiote dans sa diversité intraet interhumaine, des fonctions symbiotiques essentielles du microbiome, a ouvert la voie d’un nouveau domaine de la médecine : la médecine microbienne
Transkribus - 2023 - byzantine greek (Version 1.0.0) [Computer software]: HTR School Vienna/2023 - byzantine greek
No full textDataset(Version 1.0.0) [Computer software]σῶσον: τῆς παναγίας","Ὄτι σὸν τὸ κράτος• καὶ σοῦ ἑστιν ἡ","Εἶτα τὸ κ(ύρι)ε ἐκ(έκραξα) εἶτα τὰ στιχ(η)ρὰ· δό(ξα) καὶ νῦν","Εὐχὴ τῆς εἰσόδου","Ἑσπέρας καὶ πρωὶ καὶ μεσημβρίας,","αἰνοῦμεν εὐλογοῦμεν ευχαριστοῦ¬","μεν καὶ δεόμεθά σου δέσποτα τῶν","ἁπάντων, κατεύθυνον τὴν προσευ¬","χὴν ἡμῶν ὡς θυμίαμα ἐνώπιόν","σου• καὶ μὴ ἐκκλίνῃς τὰς καρδίας","ἡμῶν εἰς λόγους ἢ λογισμοὺς πονηρίας• ","ἀλλὰ ρῦσαι ἡμᾶς ἐκ πάντων τῶν","θηρευόντων τὰς ψυχὰς ἡμῶν• ὅ¬","τι πρὸς σὲ κ(ύρι)ε κ(ύρι)ε οἱ ὀφθαλμοὶ ἡμῶν•","καὶ ἐπὶ σοὶ ἠλπίσαμεν• μὴ καταισ¬","χύνῃς ἡμᾶς ὁ θ(εὸ)ς ἡμῶν: εἶτα εὐλογεῖ τὴν εἴσοδον","ὄτι πρέ(πει) πᾶσα δόξα• τιμὴ καὶ προσ(κύνησις)•","καὶ λέγει δόξαν• σοφία ὀρθοί• φῶς ἱλαρόν•μετὰ","δὲ τὴν εἴσοδον• βαλὼν τὴν συνήθη μετάν(οιαν) ὁ ταχθεὶς","(μον)αχ(ὸς)• ψάλλει τὸ τῆς ἡμέρας προκ(είμενον) δίστιχον•","","","εἰ δὲ εστὶ Σά(ββατον) ἑσπερ(ινάς)• λέγει το ὁ κ(ύριο)ς","Ὁ κ(ύριο)ς ἐβασίλευσεν: στίχ(ος) ἐνεδύσατο κ(ύριο)ς","στίχ(ος) καὶ γὰρ ἐστερέωσεν τὴν οἰκουμένη:","στραφεὶς δὲ ὁ ἱερ(εὺς) πρὸς δυσμᾶς, δεδεμένας","ἔχων τὰς χείρας, ἵσταται περιμένων","τὴν πλήρωσιν τοῦ προκ(ειμένου)• εἶτα βάλ(λει) μετά¬","νοιαν• καὶ ἀπέρχειται εἰς τὸν τόπον αυτοῦ·","μετὰ δὲ τὸ προκ(είμενον) δόξαν λέγει:","Εἴπομεν πάντες• ἐξ ὄλης τῆς ψυχῆς","Κ(ύρι)ε παντοκράτορ ὁ θ(εό)ς τῶν π(ατέ)ρων ἡμῶν","ἐλέησον ἡμᾶς ὁ θ(εό)ς κατὰ τὸ μέγα ἔλεός","ἔτι δεόμεθα ὑπερ τῶν εὐσεβεστάτων","καὶ ὀρθοδόξων βασιλέων:","Ἔτι δεόμεθα ὑπὲρ τοῦ ἀρχιεπισκόπου ἡμῶν","Ἔτι δεόμεθα ὑπὲρ τῶν ἀδελφῶν ἡμῶν","ἔτι δεόμεθα ὑπὲρ τῶν κτιτόρων","τῆς ἁγίας μονῆς ταύτης • καὶ μνημονεύει","Ἔτι δεόμεθα ὑπὲρ ἐλεους• ζωῆς• εἰ¬","ρήνης• ὑγείας• ἐπίσκεψαιως·• ἐνι¬","σχύσεως• συγχωρήσεως• καὶ ἀφέ¬","σεως• τῶν ἁμαρτιῶν τοῦ δούλου τοῦ:","","","Ἔτι δεόμεθα υπὲρ εὐδώσεως καὶ ἐνι¬","σχύσεως τοῦ φιλοχρήστου στρατοῦ","καὶ ὑπὲρ σ(ωτη)ρίας τοῦ περιεστῶτος λα¬","οῦ• καὶ ἀπεκδεχομένων τὸ παρὰ σοῦ","πλούσιον ἔλεος• εἷτα ἐκφωνεῖ ὁ ἱερεὺς","Ὄτι ἐλεήμων καὶ φιλάν(θρωπ)ος θ(εός) ὑπάρχεις:","καὶ ὁ λαὀς τὸ καταξίωσον: ὁ διάκονος;","Πληρώσωμεν τὴν ἑσπερινὴν δέησιν ἡμῶν;","ἀντιλαβοῦ σῶσον ἐλέησον καὶ διαφύλ(αξον)","τὴν ἑσπέραν πᾶσαν τελείαν, ἁγίαν, εἰ¬;","ρηνικὴν καὶ ἀναμάρτητον• παρὰ τῶ;","ἄγγελον εἰρήνης• πιστόν• ὁδηγὸν• φύλ(ακα):","συγγνώμην καὶ ἄφεσιν τῶν ἁμαρτι¬","ῶν• καὶ συγχώρησιν τῶν πλημμελη","τὰ τὰ καλὰ καὶ συμφέροντα ταῖς;","ψυχαῖς ἡμῶν• καὶ εἰρήνην τῷ κόσμῳ:","τὸν υπόλοιπον χρόνον τῆς ζωῆς ἡμῶν,","ἐν εἰρήνῃ καὶ ἐν μετανοία ἐκτελέσαι:","χριστιανὰ τὰ τέλη τῆς ζωῆς ἡμῶν","ἀνώδυνα• ἀνεπαίσχυντα• εἰρηνικά:","","","ἐκφώνησις ","","","τῆς παναγίας ἁχράντου ὑπὲρ εὐ¬","ὄλημένης δεσποἰνης ἡμῶν θ(εοτό)κου:","ὅτι ἁγαθὸς καὶ φιλάν(θρωπ)ος θ(εὀ)ς ὑπάρ¬","χεις• καὶ σοὶ τὴν δόξαν ἀναπέμπομεν:","εἰρἠνη πᾶσι: τὰς κεφαλὰς ἡμῶν:","εὐχὴ τῆς κεφαλοκλισίας:","Κ(ύρι)ε ὁ θ(εὸ)ς ἡμῶν• ὁ κλίνας οὐ(ρα)νοὺς καὶThe participants of the Winter School of Handwritten Text Recognition of Medieval Manuscripts Latin / Greek / Czech, Byzantine Greek Group, trained the Transkribus model "15th c. liturgical" for Byzantine Greek. The model was trained from images of the codex Dresden, SLUB A. 151. This repository contains a) transcriptions from 66 images set as "ground truth" and b) automatic transcriptions from the rest of the pages (to added later). The automatic transcriptions have an error rate of 22,3%. The errors are mostly wrong accents and breathings. To enhance searchability despite the erroneous transcription, try fuzzy search. Alternatively, you can remove the accents from the txt file (e.g. https://dev.to/djemos/removeaccents-py-5dmd)
Nyingma Perspective on Obstacles to the Revelation of Treasures (gter ma)
No full texthttps://fchnt.hypotheses.org
A Brief Note on the Northern Treasures of the Bon Tradition
No full textInternational audienceA Brief Note on the Northern Treasures of the Bon Tradition * Jean-Luc Achard (CNRS, CRCAO) According to sPa ston bsTan rgyal bzang po (15 th c.) and his Explanation of the Revelation, known as the Lamp Clarifying its Diffusion and Development (bsTan pa'i rnam bshad dar rgyas gsal sgron), the Bon tradition describes its Treasure system (gter ma) under five headings: the Northern Treasures (byang gter), the Southern Treasures (lho gter), the Central Treasures (dbus gter), the Treasures from Khams (khams gter), and the New Treasures (gter gsar). 1 In the present paper, I will briefly address the first category-the Northern Treasures-in a very cursory manner, as part of an ongoing project on Byang gter in general. 2 sPa ston's description of the Northern Treasures revolves around two main topics: the characteristics (mtshan nyid) of these Treasures and their actual designation (btags). However, he does not describe the specific features of this tradition but rather recalls its history and enumerates the texts that were found during the various revelations of what became the Northern Treasures
Verified Extraction from Coq to OCaml
No full textInternational audienceOne of the central claims of fame of the Coq proof assistant is extraction, i.e., the ability to obtain efficient programs in industrial programming languages such as OCaml, Haskell, or Scheme from programs written in Coq's expressive dependent type theory. Extraction is of great practical usefulness, used crucially e.g., in the CompCert project. However, for such executables obtained by extraction, the extraction process is part of the trusted code base (TCB), as are Coq's kernel and the compiler used to compile the extracted code. The extraction process contains intricate semantic transformation of programs that rely on subtle operational features of both the source and target language. Its code has also evolved since the last theoretical exposition in the seminal PhD thesis of Pierre Letouzey. Furthermore, while the exact correctness statements for the execution of extracted code are described clearly in academic literature, the interoperability with unverified code has never been investigated formally, and yet is used in virtually every project relying on extraction. In this paper, we describe the development of a novel extraction pipeline from Coq to OCaml, implemented and verified in Coq itself, with a clear correctness theorem and guarantees for safe interoperability. We build our work on the MetaCoq project, which aims at decreasing the TCB of Coq's kernel by reimplementing it in Coq itself and proving it correct w.r.t. a formal specification of Coq's type theory in Coq. Since OCaml does not have a formal specification, we make use of the Malfunction project specifying the semantics of the intermediate language of the OCaml compiler. Our work fills some gaps in the literature and highlights important differences between the operational semantics of Coq programs and their extracted variants. In particular, we focus on the guarantees that can be provided for interoperability with unverified code, identify guarantees that are infeasible to provide, and raise interesting open question regarding semantic guarantees that could be provided. As central result, we prove that extracted programs of first-order data type are correct and can safely interoperate, whereas for higher-order programs already simple interoperations can lead to incorrect behaviour and even outright segfaults
Mathematical modeling in the study of organisms and their parts
No full textInternational audienceMathematical modeling is a very powerful tool to understand natural phenomena. Such a tool carries its own assumptions and should always be used critically. In this chapter we highlight the key ingredients and steps of modeling and focus on their biological interpretation. In particular, we discuss the role of theoretical principles in writing models. We also highlight the meaning and interpretation of equations. The main aim of this chapter is to facilitate the interaction between biologists and mathematical modelers. We focus on the case of cell proliferation and motility in the context of multicellular organisms
Dynamical phase transition of light in time-varying nonlinear dispersive media
No full textInternational audienceWe demonstrate the existence of a prethermal dynamical phase transition (DPT) for fluctuating optical beams propagating in nonlinear dispersive media. The DPT can be probed by suddenly changing in time the dispersion and nonlinearity parameters of the medium (thus realizing a "temporal interface"), a procedure that emulates a quench in a massive model. Above a critical value of the quench identifying the transition, the fluctuating beam after the temporal interface is characterized by a correlation length that diverges algebraically at the transition. Below the critical quench, the beam exhibits an algebraic relaxation and a self-similar scaling. Our analysis also reveals a dimensional cross-over of the critical exponent, a characteristic feature of the optical DPT
