The split-and-drift random graph, a null model for speciation

We introduce a new random graph model motivated by biological questions relating to speciation. This random graph is defined as the stationary distribution of a Markov chain on the space of graphs on $\{1, \ldots, n\}$. The dynamics of this Markov chain is governed by two types of events: vertex duplication, where at constant rate a pair of vertices is sampled uniformly and one of these vertices loses its incident edges and is rewired to the other vertex and its neighbors; and edge removal, where each edge disappears at constant rate. Besides the number of vertices $n$, the model has a single parameter $r_n$. Using a coalescent approach, we obtain explicit formulas for the first moments of several graph invariants such as the number of edges or the number of complete subgraphs of order $k$. These are then used to identify five non-trivial regimes depending on the asymptotics of the parameter $r_n$. We derive an explicit expression for the degree distribution, and show that under appropriate rescaling it converges to classical distributions when the number of vertices goes to infinity. Finally, we give asymptotic bounds for the number of connected components, and show that in the sparse regime the number of edges is Poissonian.Comment: added Proposition 2.4 and formal proofs of Proposition 2.3 and 2.

Confirmation of the centrality of the Huanan market among early COVID-19 cases

The centrality of Wuhan's Huanan market in maps of December 2019 COVID-19 case residential locations, established by Worobey et al. (2022a), has recently been challenged by Stoyan and Chiu (2024, SC2024). SC2024 proposed a statistical test based on the premise that the measure of central tendency (hereafter, "centre") of a sample of case locations must coincide with the exact point from which local transmission began. Here we show that this premise is erroneous. SC2024 put forward two alternative centres (centroid and mode) to the centre-point which was used by Worobey et al. for some analyses, and proposed a bootstrapping method, based on their premise, to test whether a particular location is consistent with it being the point source of transmission. We show that SC2024's concerns about the use of centre-points are inconsequential, and that use of centroids for these data is inadvisable. The mode is an appropriate, even optimal, choice as centre; however, contrary to SC2024's results, we demonstrate that with proper implementation of their methods, the mode falls at the entrance of a parking lot at the market itself, and the 95% confidence region around the mode includes the market. Thus, the market cannot be rejected as central even by SC2024's overly stringent statistical test. Our results directly contradict SC2024's and -- together with myriad additional lines of evidence overlooked by SC2024, including crucial epidemiological information -- point to the Huanan market as the early epicentre of the COVID-19 pandemic.Comment: Reply to Stoyan and Chiu (arXiv:2208.10106

Methanol immersion reduces spherical aberration of water dipping lenses at long wavelengths used in multi-photon laser scanning microscopy

Dipping objectives were tested for multi-photon laser scanning microscopy, since their large working distances are advantageous for thick specimens and the absence of a coverslip facilitates examination of living material. Images of fluorescent bead specimens, particularly at wavelengths greater than 850 nm showed defects consistent with spherical aberration. Substituting methanol for water as the immersion medium surrounding the beads corrected these defects and produced an increase in fluorescence signal intensity. The same immersion method was applied to two representative biological samples of fixed tissue: mouse brain labeled with FITC for tubulin and mouse gut in which the Peyer’s patches were labeled with Texas Red bilosomes. Tissue morphology was well preserved by methanol immersion of both tissues; the two-photon-excited fluorescence signal was six times higher than in water and the depth of penetration of useful imaging was doubled. No modification of the microscope was needed except the provision of a ring to retain a sufficient depth of methanol for imaging

Structure sensitivity in third-harmonic generation microscopy

International audienceWe characterize experimentally the influence of sample structure and beam focusing on signal level in third-harmonic generation (THG) microscopy. In the case of a homogeneous spherical sample, the dependence of the signal on the size of the sphere can be controlled by modifying the Rayleigh length of the excitation beam. More generally, the influence of excitation focusing on the signal depends on sample geometry, allowing one to highlight certain structures within a complex system. We illustrate this point by focusing-based contrast modulation in THG images of Drosophila embryos

Accuracy of correction in modal sensorless adaptive optics.

International audienceWe investigate theoretically and experimentally the parameters governing the accuracy of correction in modal sensorless adaptive optics for microscopy. On the example of two-photon fluorescence imaging, we show that using a suitable number of measurements, precise correction can be obtained for up to 2 radians rms aberrations without optimising the aberration modes used for correction. We also investigate the number of photons required for accurate correction when signal acquisition is shot-noise limited. We show that only 10(4) to 10(5) photons are required for complete correction so that the correction process can be implemented with limited extra-illumination and associated photoperturbation. Finally, we provide guidelines for implementing an optimal correction algorithm depending on the experimental conditions

Relaxed damage threshold intensity conditions and nonlinear increase in the conversion efficiency of an optical parametric oscillator using a bi-directional pump geometry

A novel bi-directional pump geometry that nonlinearly increases the nonlinear optical conversion efficiency of a synchronously pumped optical parametric oscillator (OPO) is reported. This bi-directional pumping method synchronizes the circulating signal pulse with two counter-propagating pump pulses within a linear OPO resonator. Through this pump scheme, an increase in nonlinear optical conversion efficiency of 22% was achieved at the signal wavelength, corresponding to a 95% overall increase in average power. Given an almost unchanged measured pulse duration of 260 fs under optimal performance conditions, this related to a signal wavelength peak power output of 18.8 kW, compared with 10 kW using the traditional single-pass geometry. In this study, a total effective peak intensity pump-field of 7.11 GW/cm(2) (corresponding to 3.55 GW/cm(2) from each pump beam) was applied to a 3 mm long periodically poled lithium niobate crystal, which had a damage threshold intensity of 4 GW/cm(2), without impairing crystal integrity. We therefore prove the application of this novel pump geometry provides opportunities for power-scaling of synchronously pumped OPO systems together with enhanced nonlinear conversion efficiency through relaxed damage threshold intensity conditions

Signal epidetection in third-harmonic generation microscopy of turbid media

International audienceThird-harmonic generation (THG) imaging of thick samples or large organisms requires TH light to be epicollected through the focusing objective. In this study we first estimate the amount of backward-to-forward TH radiation created by an isolated object as a function of size and spatial frequencies in the object. Theory and model experiments indicate that no significant signal can be epidetected from a (biological) dielectric structure embedded in a transparent medium. In contrast, backward emission is observed from metal nanoparticles where THG is partly a surface effect. We then address the case of an object embedded in a turbid medium. Experiments and Monte Carlo simulations show that epidetection is possible when the absorption mean free path of harmonic light in the medium exceeds its reduced scattering length, and that epicollection efficiency critically depends on the microscope field-of-view even at shallow depths, because backscattered light is essentially diffusive. These observations provide guidelines for optimizing epidetection in third-harmonic, second-harmonic, or CARS imaging of thick tissues

Dynamic aberration correction for multiharmonic microscopy.

International audienceWe demonstrate image-based aberration correction in a third-harmonic generation (THG) microscope. We describe a robust, mostly sample-independent correction scheme relying on prior measurement of the influence of aberration modes produced by a deformable mirror on the quality of THG images. We find that using image sharpness as an image quality metric, correction of N aberration modes is achieved using 2(2N+1) measurements in a variety of samples. We also report aberration correction in combined multiharmonic and two-photon excited fluorescence experiments. Finally, we demonstrate time-dependent adaptive THG imaging in developing embryonic tissue

Room temperature magneto-optic effect in silicon light-emitting diodes

In weakly spin-orbit coupled materials, the spin-selective nature of recombination can give rise to large magnetic-field effects, for example on electro-luminescence from molecular semiconductors. While silicon has weak spin-orbit coupling, observing spin-dependent recombination through magneto-electroluminescence is challenging due to the inefficiency of emission due to silicon's indirect band-gap, and to the difficulty in separating spin-dependent phenomena from classical magneto-resistance effects. Here we overcome these challenges to measure magneto-electroluminescence in silicon light-emitting diodes fabricated via gas immersion laser doping. These devices allow us to achieve efficient emission while retaining a well-defined geometry thus suppressing classical magnetoresistance effects to a few percent. We find that electroluminescence can be enhanced by up to 300\% near room temperature in a seven Tesla magnetic field showing that the control of the spin degree of freedom can have a strong impact on the efficiency of silicon LEDs

L'Asie Mineure des géographes allemands au milieu du XIXe siècle : le projet scientifique de Carl Ritter

La présence de voyageurs dans l'Empire Ottoman est ancienne et ne date pas du XIXe siècle (Yérasimos 1991). La spécificité du début du XIXe siècle, des années 1830 en particulier, c'est de correspondre à la mise en place d'un réseau d'échange et de correspondance via les sSociétés de géographie qui sont fondées à Paris (1821), Berlin (1828) et Londres (1829). Ce moment d'institutionnalisation de la géographie repose en effet sur un partage des tâches entre géographes de cabinet et voyageurs (Surun 2006 : 128) : des instructions précises sont données aux voyageurs, les réseaux de circulation de l'information se structurent tout au long du siècle et les données collectées sur le terrain sont soumises à des procédures de validation au sein des sociétés de géographie