Asymptotic near-efficiency of the ''Gibbs-energy (GE) and empirical-variance'' estimating functions for fitting Mat{\'e}rn models -- II: Accounting for measurement errors via ''conditional GE mean''

Consider one realization of a continuous-time Gaussian process $Z$ which belongs to the Mat\' ern family with known ``regularity'' index $\nu >0$. For estimating the autocorrelation-range and the variance of $Z$ from $n$ observations on a fine grid, we studied in Girard (2016) the GE-EV method which simply retains the empirical variance (EV) and equates it to a candidate ``Gibbs energy (GE)'' i.e.~the quadratic form ${\bf z}^T R^{-1} {\bf z}/n$ where ${\bf z}$ is the vector of observations and $R$ is the autocorrelation matrix for ${\bf z}$ associated with a candidate range. The present study considers the case where the observation is ${\bf z}$ plus a Gaussian white noise whose variance is known. We propose to simply bias-correct EV and to replace GE by its conditional mean given the observation. We show that the ratio of the large-$n$ mean squared error of the resulting CGEM-EV estimate of the range-parameter to the one of its maximum likelihood estimate, and the analog ratio for the variance-parameter, have the same behavior than in the no-noise case: they both converge, when the grid-step tends to $0$, toward a constant, only function of $\nu$, surprisingly close to $1$ provided $\nu$ is not too large. We also obtain, for all $\nu$, convergence to 1 of the analog ratio for the microergodic-parameter.Comment: The previous version (version 2) considered both the case with measurement errors (also called ''nugget-effect'' or simply ''noise'') and the no-noise case. The no-noise case is now in Girard (2016) with more detailed proofs and two additional (wrt version 2) results: a consistency result is proved and the restriction $\nu \geq 1/2$ is eliminated. This version 3 is devoted to the case with measurement errors, and also gives the analogs of these two additional result

An experimental assessment of the "Gibbs-Energy and Empirical-Variance" estimating equations (via Kalman smoothing) for Matérn processes

International audienceThe problem of estimating (from n noisy observations of a single realization, at known sites) the parameters of a centered stationary Gaussian process whose autocorrelation function belongs to the Matérn class appears in many contexts (e.g. [1, 2, 3]). The recently proposed CGEM-EV method [4] only requires the computation of several conditional means, at the observation sites, corresponding to candidate values for the Matérn parameters. In dimension 1 and when the “Matérn differentiability” parameter is fixed to k + 1/2 with k integer (an often-used value is k = 0 or k = 1, see e.g. [3], [1], [6], [7], [8]), each of these conditional means reduces to a Kalman smoothing.An R implementation of CGEM-EV for this context is presented : it is built on the R-package dlm [5]. It proves to be quite fast, even for high-frequency sampling (e.g. n = 8196), and an empirical comparison with the classical maximum likelihood estimator confirms the near- efficiency results of [4]

Les écoles d'astrostatistique " Statistics for Astrophysics "

National audienceL'astrophysique est une science physique basée sur l'observation, s'appuyant sur des instruments de détection toujours plus gigantesques et perfectionnés. La quantité de données recueillies impose des traitements statistiques fiables et efficaces. L'objectif des écolesd'astrostatistique est de donner les compétences nécessaires aux participants astrophysiciens pour entreprendre par eux-mêmes des analyses statistiques. Depuis 2013, les trois sessions de cette école ont été consacrées successivement aux méthodes de régression, classification, puis aux approches bayésiennes. Nous présentons dans cette communication les retours de notre expérience d'organisateurs

Upper Cretaceous amber from Vendée, north-western France:Age dating and geological, chemical, and palaeontological characteristics

International audienceThe Upper Cretaceous lignite deposits of La Garnache, Vendée (western France), consist of two lignitic clay series, Garnache 1 and Garnache 2, separated by a fault. The first series cropped out to the south of the fault during road works until 2002 but is now covered by an embankment. It has provided numerous pieces of amber containing arthropod and microorganism inclusions. The second lignitic series, exposed to the north of the fault, is rich in fossil wood but devoid of amber. Palynological analysis of Garnache 1 revealed several Normapolles species belonging to the genera Atlantopollis, Complexiopollis, Osculapollis, Plicapollis and Trudopollis, but larger forms typical of Senonian deposits are absent. By contrast, Garnache 2 proved to be dominated taxonomically and numerically by spores (Appendicisporites, Camarozonosporites, Gleicheniidites, Patellasporites, Stereisporites), associated with a few gymnosperm (Cerebropollenites, Phyllocladidites, Classopollis) and angiosperm (Liliacidites, Retitricolpites and a single specimen of the Normapolles Complexiopollis) taxa. Garnache 1 is, therefore, younger than Garnache 2, the latter being clearly Cenomanian in age whereas Garnache 1 is more likely to be Turonian. Lignitic clay of Garnache 1 contains numerous translucent, orange to red, pieces of amber. Vendean amber is rich in aquatic arthropods, such as tanaids and epicarideans (Crustacea), as well as marine or brackish siliceous microorganisms such as diatoms and sponge spicules. These aquatic inclusions indicate that resin-producing trees grew along and close to the seashore. The amber-bearing clay was deposited in a calm, estuarine or lagoonal, muddy environment

Characterization of a small tRNA-binding protein that interacts with the archaeal proteasome complex

Authors acknowledge financial support from the French Agence Nationale de la Recherche (grant [ANR-18-CE11-0018-01] to B.F. and [ANR-16-CE12-0016-01] to B.C.O). This work used the platforms of the Grenoble Instruct-ERIC Centre (ISBG: UMS3518 CNRS-CEA-UGA-EMBL) with support from FRISBI (ANR-10-INBS-05-02) and GRAL, a project of the University Grenoble Alpes graduate school (Ecoles Universitaires de Recherche) CBH-EUR-GS (ANR-17-EURE-0003) within the Grenoble Partnership for Structural Biology. The IBS Electron Microscope facility is supported by the Auvergne Rhône-Alpes Region, the Fonds Feder, the Fondation pour la Recherche Médicale and GIS-IBiSA.The proteasome system allows the elimination of functional or structurally impaired proteins. This includes the degradation of nascent peptides. In Archaea, how the proteasome complex interacts with the translational machinery remains to be described. Here, we characterised a small orphan protein, Q9UZY3 (Uniprot ID) conserved in Thermococcales. The protein was identified in native pull-down experiments using the proteasome regulatory complex (PAN) as bait. X-ray crystallography and SAXS experiments revealed that the protein is monomeric and adopts a β-barrel core structure with an Oligonucleotide/oligosaccharide-Binding (OB) fold, typically found in translation elongation factors. Mobility shift experiment showed that Q9UZY3 displays tRNA binding properties. Pull-downs, co-immunoprecipitation and ITC studies revealed that Q9UZY3 interacts in vitro with PAN. Native pull-downs and proteomic analysis using different versions of Q9UZY3 showed that the protein interacts with the assembled PAN-20S proteasome machinery in Pyrococcus abyssi cellular extracts. The protein was therefore named Pbp11, for Proteasome Binding Protein of 11 kDa. Interestingly, the interaction network of Pbp11 also includes ribosomal proteins, tRNA processing enzymes and exosome subunits dependent on Pbp11's N-terminal domain that was found to be essential for tRNA binding. Together these data suggest that Pbp11 participates in an interface between the proteasome and the translational machinery.Publisher PDFPeer reviewe

Pandemic stress and SARS-CoV-2 infection are associated with pathological changes at the maternal-fetal interface

Introduction The reported effects of SARS-CoV-2 on pregnancy outcomes are conflicting; studies frequently overlook the placenta, which is critical for the health of the mother and infant(s). This study aimed to determine the effect of pandemic stress ± SARS CoV-2 infection on placental histopathology. Methods Women were recruited in Canada (n = 69); France (n = 21) or in the UK (n = 25), between March and October 2020. Historic controls (N = 20) were also included. Placenta and fetal membrane samples were collected rapidly after delivery and were fixed and stained for histopathological analysis. Maternal demographical data and obstetric outcomes were recorded. Results Over 80% of the placentas from SARS-CoV-2+ pregnancies had histopathological abnormalities: predominantly structural (71–86%) or inflammatory (9–22%), depending on geographical location. Excessive fibrin was seen in all sites, whereas deciduitis (Canada), calcifications (UK), agglutinations and chorangiosis (France) predominated in different locations. The frequency of abnormalities was significantly higher than in SARS-CoV-2 negative women (50%, p < 0.05). Demographic and obstetric data were similar in the SARS-CoV-2+ women across all sites - characterised by predominantly Black/Middle Eastern women, and women with elevated body mass index. Discussion Overall, the frequency of placental abnormalities is increased in SARS-CoV-2+ women, but the incidence of placental abnormalities is also higher in SARS-CoV-2- women that gave birth during the pandemic, which highlights the importance of appropriate control groups to ascertain the roles of pandemic stress and SARS-CoV-2 infection on the placenta and pregnancy outcomes

Assessment of the impacts of pets on human health and quality of life

The interest for animal-associated activities and therapy is growing and the impact of these projects on health and quality of life needs to be assessed. Unfortunately, there are major variations in the methodology, objectives and indicators used in these studies. An analysis of the main published articles revealed the limitations of population-based observation studies. Cost-effectiveness studies are much more useful, as long as they comply with the principles of such studies. The main issues, i.e. the nature of what is to be demonstrated, how costs and efficacy are measured, and the cultural background of the project, need to be addressed with special care.Le développement des projets d'activité associant l'animal dans un but thérapeutique rend nécessaire une évaluation de l'impact de ces projets sur la santé et la qualité de vie. Malheureusement les études dans ce domaine sont hétérogènes tant dans leurs qualités méthodologiques, leurs objectifs que dans les indicateurs retenus. L'analyse des principales études publiées invite à considérer avec prudence les études d'observation populationnelles. Les études de type coût/efficacité, ou mieux coût/effectivité, sont à privilégier à condition de bien en respecter les principes. Les questions essentielles portent sur la nature de ce que l'on veut mettre en évidence, la façon de construire les mesures de coût et d'efficacité et le contexte culturel du projet. Elles doivent être résolues avec attention