Achieving dietary recommendations and reducing greenhouse gas emissions : modelling diets to minimise the change from current intakes

Acknowledgements We are grateful to Mr Hubert Ehlert for extending the work on the coding for the linear programming and to Mrs Jennifer Loe for preparing the dataset matching the food consumption data with the GHGE data. Funding This work was supported as part of the research programme funded by the Scottish Government Rural and Environment Science and Analytical Services Division [RESAS].Peer reviewedPublisher PD

Time delays in the diagnosis and treatment of Fabry disease

ABSTRACT Background: The high variability in clinical manifestations of Fabry disease can lead to delays between symptom onset and correct diagnosis, and between correct diagnosis and initiation of enzyme replacement therapy. We investigated whether these delays have improved in recent years. Methods: Data were analyzed from the Fabry Outcome Survey (FOS; Shire; extracted August 2013) for “index patients”, defined as the first patient diagnosed with Fabry disease from a family with several or no additional members registered in FOS. Results: Periods analyzed: 2001–2006 versus 2007–2013, in patients overall and from Europe versus the rest of the world (ROW). Overall, 598 patients were diagnosed within the study periods. Median age (95% CI) at symptom onset in 2001–2006 and 2007–2013 was 7.0 (5.0–11.0) and 9.0 (6.0–11.0) in children, and 21.0 (15.0–28.0) and 31.0 (26.0–35.0) in adults, respectively. Overall, the delay in diagnosis did not improve, despite showing a trend towards earlier diagnosis in adults (median 14.0 [95% CI 9.0–20.0] vs. 10.5 [8.0–13.0] years) and children (5.0 [1.0–9.0] vs. 4.0 [0.0–8.0] years). In contrast, the delay in treatment onset significantly decreased from 2001–2006 to 2007–2013 in children (4.3 [2.0–7.0] vs. 1.0 [0.8–1.4] year; p < 0.001) and adults (2.1 [1.3–3.2] vs. 0.9 [0.8–1.1] years; p < 0.001). Geographically, the delay in treatment onset significantly decreased in the ROW among children (5.3 [4.2–8.0] vs. 1.0 [0.8–1.4] year; p < 0.001) and adults (5.4 [4.8–6.0] vs. 1.1 [0.9–1.1] year; p < 0.001), but it did not change in Europe. Conclusion: We found that the delay in diagnosis has not improved substantially whereas the delay in treatment onset has improved in recent years.pre-print519 K

ProCARs: Progressive Reconstruction of Ancestral Gene Orders

International audienceBackground: In the context of ancestral gene order reconstruction from extant genomes, there exist two main computational approaches: rearrangement-based, and homology-based methods. The rearrangement-based methods consist in minimizing a total rearrangement distance on the branches of a species tree. The homology-based methods consist in the detection of a set of potential ancestral contiguity features, followed by the assembling of these features into Contiguous Ancestral Regions (CARs). Results: In this paper, we present a new homology-based method that uses a progressive approach for both the detection and the assembling of ancestral contiguity features into CARs. The method is based on detecting a set of potential ancestral adjacencies iteratively using the current set of CARs at each step, and constructing CARs progressively using a 2-phase assembling method. We show the usefulness of the method through a reconstruction of the boreoeutherian ancestral gene order, and a comparison with three other homology-based methods: AnGeS, InferCARs and GapAdj. The program is written in Python, and the dataset used in this paper are available at http://bioinfo.lifl.fr/procars/

findings from the Icatibant Outcome Survey

Background Patients with hereditary angioedema (HAE) due to C1-inhibitor deficiency (C1-INH-HAE) experience recurrent attacks of cutaneous or submucosal edema that may be frequent and severe; prophylactic treatments can be prescribed to prevent attacks. However, despite the use of long-term prophylaxis (LTP), breakthrough attacks are known to occur. We used data from the Icatibant Outcome Survey (IOS) to evaluate the characteristics of breakthrough attacks and the effectiveness of icatibant as a treatment option. Methods Data on LTP use, attacks, and treatments were recorded. Attack characteristics, treatment characteristics, and outcomes (time to treatment, time to resolution, and duration of attack) were compared for attacks that occurred with versus without LTP. Results Data on 3228 icatibant-treated attacks from 448 patients with C1-INH-HAE were analyzed; 30.1% of attacks occurred while patients were using LTP. Attack rate, attack severity, and the distribution of attack sites were similar across all types of LTP used, and were comparable to the results found in patients who did not receive LTP. Attacks were successfully treated with icatibant; 82.5% of all breakthrough attacks were treated with a single icatibant injection without C1-INH rescue medication. Treatment outcomes were comparable for breakthrough attacks across all LTP types, and for attacks without LTP. Conclusions Patients who use LTP should be aware that breakthrough attacks can occur, and such attacks can be severe. Thus, patients with C1-INH-HAE using LTP should have emergency treatment readily available. Data from IOS show that icatibant is effective for the treatment of breakthrough attacks. Trial Registration NCT0103496

Was the last bacterial common ancestor a monoderm after all?

The very nature of the last bacterial common ancestor (LBCA), in particular the characteristics of its cell wall, is a critical issue to understand the evolution of life on earth. Although knowledge of the relationships between bacterial phyla has made progress with the advent of phylogenomics, many questions remain, including on the appearance or disappearance of the outer membrane of diderm bacteria (also called Gram-negative bacteria). The phylogenetic transition between monoderm (Gram-positive bacteria) and diderm bacteria, and the associated peptidoglycan expansion or reduction, requires clarification. Herein, using a phylogenomic tree of cultivated and characterized Bacteria as an evolutionary framework and a literature review of their cell-wall characteristics, we used Bayesian ancestral state reconstruction to infer the cell-wall architecture of the LBCA. With the same phylogenomic tree, we further revisited the evolution of the division and cell-wall synthesis (dcw) gene cluster using homology- and model-based methods. Finally, extensive similarity searches were carried out to determine the phylogenetic distribution of the genes involved with the biosynthesis of the outer membrane in diderm bacteria. Quite unexpectedly, our analyses suggest that all cultivated and characterized bacteria might have evolved from a common ancestor with a monoderm cell-wall architecture. If true, this would indicate that the appearance of the outer membrane was not a unique event and that selective forces have led to the repeated adoption of such an architecture. Due to the lack of phenotypic information, our methodology cannot be applied to all extant bacteria. Consequently, our conclusion might change once enough information is made available to allow the use of an even more diverse organism selection

A New High-Throughput Tool to Screen Mosquito-Borne Viruses in Zika Virus Endemic/Epidemic Areas

International audienceMosquitoes are vectors of arboviruses affecting animal and human health. Arboviruses circulate primarily within an enzootic cycle and recurrent spillovers contribute to the emergence of human-adapted viruses able to initiate an urban cycle involving anthropophilic mosquitoes. The increasing volume of travel and trade offers multiple opportunities for arbovirus introduction in new regions. This scenario has been exemplified recently with the Zika pandemic. To incriminate a mosquito as vector of a pathogen, several criteria are required such as the detection of natural infections in mosquitoes. In this study, we used a high-throughput chip based on the BioMark™ Dynamic arrays system capable of detecting 64 arboviruses in a single experiment. A total of 17,958 mosquitoes collected in Zika-endemic/epidemic countries (Brazil, French Guiana, Guadeloupe, Suriname, Senegal, and Cambodia) were analyzed. Here we show that this new tool can detect endemic and epidemic viruses in different mosquito species in an epidemic context. Thus, this fast and low-cost method can be suggested as a novel epidemiological surveillance tool to identify circulating arboviruses

Vers une méthode de conception HYGRO-thermique des BATiments performants : démarche du projet HYGRO-BAT

Cet article présente la démarche mise en oeuvre dans le projet collaboratif ANR Hygrobat, qui vise à donner des outils pour quantifier de manière fiable l'impact des transferts de masse sur les transferts de chaleur dans les parois de bâtiments comprenant des matériaux fortement hygroscopiques. Les matériaux sélectionnés dans ce projets (fibre de bois, bois massif, OSB) ont été soigneusement caractérisés. Leurs propriétés hygrothermiques ont été mesurées en laboratoire, puis ils ont été mis en oeuvre dans des parois, soumises à des conditions aux limites de variées. L'originalité de l'étude réside dans : (i) la démarche "pas à pas" de complexité croissante, partant des caractérisations d'un seul matériau en conditions stationnaires, jusqu'aux mesures sur une paroi multicouche en climat réel ; (ii) les vérifications croisées de mesures expérimentales, qui sont effectuées dans deux des laboratoires partenaires du projet, parfois sur des dispositifs différents ; (iii) association des benchmarks expérimentaux et numérique

Geographical and temporal distribution of SARS-CoV-2 clades in the WHO European Region, January to June 2020

We show the distribution of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) genetic clades over time and between countries and outline potential genomic surveillance objectives. We applied three genomic nomenclature systems to all sequence data from the World Health Organization European Region available until 10 July 2020. We highlight the importance of real-time sequencing and data dissemination in a pandemic situation, compare the nomenclatures and lay a foundation for future European genomic surveillance of SARS-CoV-2