A uniform analysis of HD209458b Spitzer/IRAC lightcurves with Gaussian process models

We present an analysis of Spitzer/IRAC primary transit and secondary eclipse lightcurves measured for HD209458b, using Gaussian process models to marginalise over the intrapixel sensitivity variations in the 3.6 micron and 4.5 micron channels and the ramp effect in the 5.8 micron and 8.0 micron channels. The main advantage of this approach is that we can account for a broad range of degeneracies between the planet signal and systematics without actually having to specify a deterministic functional form for the latter. Our results do not confirm a previous claim of water absorption in transmission. Instead, our results are more consistent with a featureless transmission spectrum, possibly due to a cloud deck obscuring molecular absorption bands. For the emission data, our values are not consistent with the thermal inversion in the dayside atmosphere that was originally inferred from these data. Instead, we agree with another re-analysis of these same data, which concluded a non-inverted atmosphere provides a better fit. We find that a solar-abundance clear-atmosphere model without a thermal inversion underpredicts the measured emission in the 4.5 micron channel, which may suggest the atmosphere is depleted in carbon monoxide. An acceptable fit to the emission data can be achieved by assuming that the planet radiates as an isothermal blackbody with a temperature of $1484\pm 18$ K.Comment: 18 pages, 5 figures, 6 tables. Accepted by MNRA

Quasi-normal modes and their overtones at the common horizon in a binary black hole merger

It is expected that all astrophysical black holes in equilibrium are well described by the Kerr solution. Moreover, any black hole far away from equilibrium, such as one initially formed in a compact binary merger or by the collapse of a massive star, will eventually reach a final equilibrium Kerr state. At sufficiently late times in this process of reaching equilibrium, we expect that the black hole is modeled as a perturbation around the final state. The emitted gravitational waves will then be damped sinusoids with frequencies and damping times given by the quasi-normal mode spectrum of the final Kerr black hole. An observational test of this scenario, often referred to as black hole spectroscopy, is one of the major goals of gravitational wave astronomy. It was recently suggested that the quasi-normal mode description including the higher overtones might hold even right after the remnant black hole is first formed. At these times, the black hole is expected to be highly dynamical and non-linear effects are likely to be important. In this paper we investigate this remarkable scenario in terms of the horizon dynamics. Working with high accuracy simulations of a simple configuration, namely the head-on collision of two non-spinning black holes with unequal masses, we study the dynamics of the final common horizon in terms of its shear and its multipole moments. We show that they are indeed well described by a superposition of ringdown modes as long as a sufficiently large number of higher overtones are included. This description holds even for the highly dynamical final black hole shortly after its formation. We discuss the implications and caveats of this result for black hole spectroscopy and for our understanding of the approach to equilibrium.Comment: 26p., 21 figures, 1 table. To be submitted. Comments welcom

Oligosaccharide Chromatographic Techniques for Quantitation of Structural Process-Related Impurities in Heparin Resulting From 2-O Desulfation

Heparin is a widely-used intravenous anticoagulant comprising a complex mixture of highly-sulfated linear polysaccharides of repeating sequences of uronic acids (either iduronic or glucuronic) 1->4 linked to D-glucosamine with specific sulfation patterns. Preparation of crude heparin from mammalian mucosa involves protease digestion with alcalase under basic conditions (pH ≥ 9) and high temperature (>50°C) and also oxidation. Under such conditions, side reactions including the ubiquitous 2-O desulfation occur on the heparin backbone yielding non-endogenous disaccharides within polysaccharide chains. Whatever the process used for its manufacture, some level of corresponding degradation impurities is therefore expected to be found in heparin and the derived Low Molecular Weight Heparins. These impurities should be monitored to control the quality of the final therapeutic product. Two anion exchange chromatography techniques were used to analyze heparin samples exhaustively or partially depolymerized with heparinases and determine the proportions of non-endogenous disaccharides generated by side reactions during the manufacturing process (epoxides and galacturonic moieties). We also present data from a case study of marketed heparin. Current heparin sodium monographs do not directly address process impurities related to modification of the structure of heparin. Although desulfation reduces the overall biological potency, we found that heparin with an average of one modified disaccharide per chain can still comply with the USP or Ph. Eur. heparin sodium monographs requirements. We have implemented disaccharide analysis to monitor the quality of this product on a risk basis

Genomic analysis of the causative agents of coccidiosis in domestic chickens

Global production of chickens has trebled in the past two decades and they are now the most important source of dietary animal protein worldwide. Chickens are subject to many infectious diseases that reduce their performance and productivity. Coccidiosis, caused by apicomplexan protozoa of the genus Eimeria, is one of the most important poultry diseases. Understanding the biology of Eimeria parasites underpins development of new drugs and vaccines needed to improve global food security. We have produced annotated genome sequences of all seven species of Eimeria that infect domestic chickens, which reveal the full extent of previously described repeat-rich and repeat-poor regions and show that these parasites possess the most repeat-rich proteomes ever described. Furthermore, while no other apicomplexan has been found to possess retrotransposons, Eimeria is home to a family of chromoviruses. Analysis of Eimeria genes involved in basic biology and host-parasite interaction highlights adaptations to a relatively simple developmental life cycle and a complex array of co-expressed surface proteins involved in host cell binding

Mortality and pulmonary complications in patients undergoing surgery with perioperative SARS-CoV-2 infection: an international cohort study

Background: The impact of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) on postoperative recovery needs to be understood to inform clinical decision making during and after the COVID-19 pandemic. This study reports 30-day mortality and pulmonary complication rates in patients with perioperative SARS-CoV-2 infection. Methods: This international, multicentre, cohort study at 235 hospitals in 24 countries included all patients undergoing surgery who had SARS-CoV-2 infection confirmed within 7 days before or 30 days after surgery. The primary outcome measure was 30-day postoperative mortality and was assessed in all enrolled patients. The main secondary outcome measure was pulmonary complications, defined as pneumonia, acute respiratory distress syndrome, or unexpected postoperative ventilation. Findings: This analysis includes 1128 patients who had surgery between Jan 1 and March 31, 2020, of whom 835 (74·0%) had emergency surgery and 280 (24·8%) had elective surgery. SARS-CoV-2 infection was confirmed preoperatively in 294 (26·1%) patients. 30-day mortality was 23·8% (268 of 1128). Pulmonary complications occurred in 577 (51·2%) of 1128 patients; 30-day mortality in these patients was 38·0% (219 of 577), accounting for 81·7% (219 of 268) of all deaths. In adjusted analyses, 30-day mortality was associated with male sex (odds ratio 1·75 [95% CI 1·28–2·40], p\textless0·0001), age 70 years or older versus younger than 70 years (2·30 [1·65–3·22], p\textless0·0001), American Society of Anesthesiologists grades 3–5 versus grades 1–2 (2·35 [1·57–3·53], p\textless0·0001), malignant versus benign or obstetric diagnosis (1·55 [1·01–2·39], p=0·046), emergency versus elective surgery (1·67 [1·06–2·63], p=0·026), and major versus minor surgery (1·52 [1·01–2·31], p=0·047). Interpretation: Postoperative pulmonary complications occur in half of patients with perioperative SARS-CoV-2 infection and are associated with high mortality. Thresholds for surgery during the COVID-19 pandemic should be higher than during normal practice, particularly in men aged 70 years and older. Consideration should be given for postponing non-urgent procedures and promoting non-operative treatment to delay or avoid the need for surgery. Funding: National Institute for Health Research (NIHR), Association of Coloproctology of Great Britain and Ireland, Bowel and Cancer Research, Bowel Disease Research Foundation, Association of Upper Gastrointestinal Surgeons, British Association of Surgical Oncology, British Gynaecological Cancer Society, European Society of Coloproctology, NIHR Academy, Sarcoma UK, Vascular Society for Great Britain and Ireland, and Yorkshire Cancer Research

Inhomogeneous Relativistic Cosmology : nonperturbative models and spatial averaging of the Einstein equations

Dans le modèle standard de la cosmologie, la dynamique globale de l'Univers est modélisée par l'intermédiaire d'un espace-temps de référence (ou de fond) fortement symétrique, admettant des sections spatiales homogènes et isotropes. Le couplage entre les sources fluides, homogènes, et l'expansion globale, y est déterminé par les équations d'Einstein de la Relativité Générale. La formation de structures inhomogènes de matière peut également être décrite dans ce modèle. Selon l'époque et l'échelle considérées, cette description est effectuée soit à l'aide d'un schéma perturbatif relativiste supposant une faible déviation de chaque grandeur par rapport au fond homogène imposé, soit au moyen d'une approche newtonienne au sein du même fond en expansion. L'interprétation des observations dans ce modèle suggère cependant une accélération inattendue de l'expansion, qui requiert une nouvelle composante énergétique mal comprise, l' «Énergie Noire», en plus de la Matière Noire. La cosmologie inhomogène a pour but de lever les restrictions imposées par ces modèles sur la géométrie et sur les sources sans sortir du cadre de la Relativité Générale. Cela peut notamment permettre d'améliorer le modèle de formation des structures pour prendre en compte de fortes déviations par rapport à l'homogénéité dans la distribution de matière et dans la géométrie. Cela permet également d'étudier les conséquences dynamiques, appelées effets de rétroaction («backreaction»), du développement local de telles inhomogénéités sur l'expansion à de plus grandes échelles. De telles rétroactions peuvent alors reproduire, au moins partiellement, les comportements attribués à l'Énergie Noire ou à la Matière Noire. Au cours de mon travail de thèse sous la direction de Thomas Buchert, j'ai étudié plusieurs aspects analytiques de la cosmologie inhomogène en Relativité Générale. Je présente ci-dessous les résultats de travaux au sein de collaborations, auxquels j'ai apporté des contributions majeures dans le cadre de la thèse. Je me suis tout d'abord concentré sur l'écriture d'un schéma d'approximation relativiste lagrangien, pour décrire la dynamique locale des structures jusqu'à un régime non-linéaire, dans des fluides parfaits barotropes irrotationnels. Je me suis ensuite intéressé à la description effective de fluides inhomogènes admettant un tenseur d'énergie-impulsion général ainsi que de la vorticité, au moyen de deux schémas possibles de moyenne spatiale. Ces schémas s'appliquent à un choix quelconque des hypersurfaces spatiales sur lesquelles moyenner, et fournissent pour chacun de ces choix un système d'équations d'évolution effectives, présentant plusieurs termes de rétroaction, pour un domaine d'intégration suivant la propagation des sources. Cela permet une discussion qualitative de la dépendance au choix du feuilletage des équations moyennes et des rétroactions. J'ai également étudié la réécriture de ces schémas de moyennes et équations d'évolution, et d'autres obtenus de façon similaire, sous une forme unifiée et manifestement 4-covariante. Ce dernier résultat permettra une étude plus explicite de la dépendance au feuilletageIn the standard model of cosmology, the global dynamics of the Universe is modelled via a highly symmetric background spacetime with homogeneous and isotropic spatial sections. The coupling of the homogeneous fluid sources to the overall expansion is then determined by the Einstein equations of General Relativity. In addition, the formation of inhomogeneous matter structures is described either via a relativistic perturbation scheme assuming small deviations of all fields to the prescribed homogeneous background, or using Newtonian dynamics within the same expanding background, depending on the scale and epoch. However, the interpretation of observations within this model calls for an unexpectedly accelerated expansion requiring a poorly-understood `Dark Energy' component, in addition to Dark Matter. Inhomogeneous cosmology aims at relaxing the restrictions of these models on the geometry and sources while staying within the framework of General Relativity. It can allow, in particular, for an improved modelling of the formation of structures accounting for strong deviations from homogeneity in the matter distribution and the geometry. It can also study the dynamical consequences, or backreaction effects, of the development of such inhomogeneities on the expansion of larger scales. Such a backreaction may then reproduce, at least partially, the behaviours attributed to Dark Energy or Dark Matter. During my PhD under the direction of Thomas Buchert, I have been working on several analytical aspects of general-relativistic inhomogeneous cosmology. I present below the results of collaborations in which I played a major role in the context of the PhD. I first focussed on the expression of a relativistic Lagrangian approximation scheme for the description of the local dynamics of structures up to a nonlinear regime in irrotational perfect barotropic fluids. I then considered the effective description of inhomogeneous fluids with vorticity and a general energy-momentum tensor in terms of two possible schemes of spatial averaging. These schemes are applicable to any choice of spatial hypersurfaces of averaging, providing for each choice a set of effective evolution equations, featuring several backreaction terms, for an averaging region comoving with the sources. This allows for a qualitative discussion of the dependence of the average equations and backreactions on the foliation choice. I also studied the rewriting of such averaging schemes and evolution equations under a unified and manifestly 4-covariant form. This latter result will allow for a more explicit investigation of foliation dependenc