On the assessment of precipitation extremes in reanalysis and ensemble forecast datasets

Precipitation extremes can trigger natural hazards with large impacts. The accurate quantification of the probability and the prediction of the occurrence of heavy precipitation events is crucial for the mitigation of precipitation-related hazards. This PhD thesis provides methods for the assessment of precipitation extremes. The methods are applied to different gridded datasets. The framework of extreme value theory, and more precisely the extended generalized Pareto distribution (EGPD), is used to quantify precipitation distributions. Chapter 2 compares ERA-5 precipitation dataset with observation-based datasets and identifies the regions of low or high agreement of ERA-5 precipitation with observations. ERA-5 is a reanalysis dataset, i.e. a reconstruction of the past weather obtained by combining past observations with weather forecast models. The strengths of reanalysis precipitation fields are the regular spatio-temporal coverage and the consistence with the data on the atmospheric circulation from the reanalysis. However, precipitation in ERA-5 stem from short-term forecasts and the precipitation data calculation does not include observed precipitation. Therefore a comparison with observational datasets is needed to assess the quality of the precipitation data. We compare ERA-5 precipitation with two observation-based gridded datasets: EOBS (station-based) over Europe and CMORPH (satellite-based) globally. Both intensity and occurrence of precipitation extremes are compared. We measure the co-occurrence of extremes between ERA-5 and the observational datasets with a hit rate of binary extreme events. We find a decrease in the hit rate with increasing rarity of events. Over Europe, the hit rate is rather homogeneous except near arid regions where it has a larger variability. In the global comparison, the midlatitude oceans are the regions with the largest agreement for the occurrence of extremes between the satellite observations and the reanalysis dataset. The areas with the largest disagreement are the tropics, especially over Africa. We compare the precipitation intensity extremes between ERA-5 and the observational datasets using confidence intervals on the estimation of extreme quantiles and a test based on the Kullback-Leibler divergence. Both the confidence intervals and the Kullback-Leibler divergence calculations are based on the fitting of the precipitation distribution with the EGPD. The quantile comparison indicates an overlap of the confidence intervals on extreme quantiles (with a probability of non-exceedance of 0.9) for about 85% of the grid points over Europe and 72% globally. The regions with non-overlapping confidence intervals between ERA-5 and EOBS correspond to regions where the observation coverage is sparse and therefore where EOBS is more uncertain. The two datasets have a good agreement over countries with dense observational coverage. ERA-5 and CMORPH precipitation intensities agree well over the midlatitudes. The tropics are a region of disagreement: ERA-5 underestimates quantiles for heavy precipitation compared to CMORPH. In Chapter 3, we provide return levels of heavy precipitation events with regional fittings of the EGPD. The goal of this chapter is to develop a regional fitting method being a good trade-off between a robust estimation of the distribution and parsimony of the model, with a focus on precipitation extremes. We apply the method to ERA-5 precipitation data over Europe. This area of the dataset contains more than 20,000 grid points. A local fit of EGPD distributions for all grid points in Europe would therefore imply estimating a large number of parameters. To reduce the number of estimated parameters, we identify homogeneous regions in terms of extreme precipitation behaviors. Locations with a similar distribution of extremes (up to a normalizing factor) are first clustered with a partitioning-around-medoid (PAM) procedure. The distance used in the clustering procedure is based on a scale-invariant ratio of probability-weighted moments focusing on the upper tail of the distribution. We then fit an EGPD with a constraint: only one parameter (out of three) is allowed to vary within a homogeneous region. The outputs of Chapter 3 are 1) a step-by-step blueprint that leverages a recently developed and fast clustering algorithm to infer return level estimates over large spatial domains and 2) maps of return levels over Europe for different return periods and seasons. The relatively parsimonious model with only one spatially varying parameter can compete well against statistical models of higher complexity. The last part of this thesis (Chapter 4) evaluates the prediction skill of operational forecasts on a subseasonal (S2S) time scale. Good forecasts of extreme precipitation are crucial for warnings and subsequent mitigation of natural hazards impacts. The skill of extreme precipitation forecasts is assessed over Europe in the S2S forecast model produced by the European Centre for Medium-Range Weather Forecasts. ERA-5 precipitation is used as a reference. Extreme events are defined as daily precipitation exceeding the 95th seasonal percentile. The precipitation data is transformed into a binary dataset (threshold exceedance vs. no threshold exceedance). The percentiles are calculated independently for the forecast and the reference dataset: the direct comparison of dataset-specific quantiles removes potential biases in the data. The Brier score is computed as a reference metric to quantify the skill of the forecast model. In addition to the Brier score, a binary loss function is used to focus the verification on the occurrence of the extreme, discarding the days when the daily precipitation is not extreme, in both the forecast and the verification datasets. A daily and local verification of extremes is conducted; the analysis is extended further by aggregating the data in space and time. Results consistently show higher skill in winter compared to summer. Portugal, Norway and the South of the Alps are the regions with the highest skill in general. The Mediterranean region also presents a relatively good skill in winter. The spatial and temporal aggregation increases the skill. Each part of this thesis provides methods to model and evaluate precipitation extremes. The outcome of Chapter 2 is an evaluation of ERA-5 precipitation. Europe is found to be a region of good performance in this dataset. ERA-5 is therefore used to apply the regionalized estimation of return levels developed in Chapter 3. Furthermore, the reanalysis dataset is used as a reference for the estimation of the S2S forecast skill for precipitation extremes, in Chapter 4. The appendix contains the additional articles in which I was involved during my PhD project, as a lead author or as a coauthor

Una lettura dell'istruzione Cor Orans sulla vita contemplativa femminile: sfide e prospettive

SOMMARIO: 1. Premessa - 2. Natura del documento - 3. I destinatari della CO - 4. L’autonomia giuridica dei monasteri - 5. L’obbligo di aderire a una federazione - 6. La formazione comune obbligatoria - 7. Il rilassamento della clausura - 8. Qual è la mens legislatoris?An Analysis of the Instruction Cor Orans on Women's Contemplative Life: Challenges and PerspectivesABSTRACT: This article is a commentary of Cor Orans, the Implementing Instruction of the Apostolic Constitution “Vultum Dei Quaerere” on Women’s Contemplative Life, published in 2018 by the Congregation for Institutes of Consecrated Life and Societies of Apostolic Life. This Instruction has the character of a real pontifical law, in many aspects disrupting the law which hitherto governed enclosed nuns. By constraining every Monastery to be part of a federation, which although presented as a communion structure, in fact resembles a genuine structure of government, the Instruction harms the autonomy of Monasteries. This mandatory federal setup goes hand in hand with a slackening of the enclosure, and will give rise to a decrease in religious observance. The article further proceeds to outline the mens legislatoris, found between the pursuit of communion and shortage management, and underlines the reductive and materialistic view of contemplative life exhibited by the document. Finally, the article underlines the determination with which the Dicastery intends to apply the new norms, a determination which shows little consideration for the principle of legality

Antiquité tardive en région Centre-Val de Loire (AnTaRec)

Marie-Pierre Chambon, Laurent Fournier et Édith Rivoire (Inrap), porte sur l’étude de l’Antiquité tardive en région Centre. La fourchette chronologique retenue est large puisqu’elle couvre la période allant de la seconde moitié du iiie s. apr. J.-C. à la première moitié du vie s. apr. J.-C. La zone géographique étudiée est la région Centre-Val de Loire dans ses limites administratives actuelles. L’objectif de ce PCR est de regrouper l’ensemble des chercheurs intéressés par cette période quel ..

POWERbreathe® Inspiratory Muscle Training in Amyotrophic Lateral Sclerosis.

Inspiratory muscle training may benefit respiratory function, cardiocirculatory parameters, quality of life and functionality in neuromuscular diseases. This pilot study aimed to demonstrate the POWERbreathe® inspiratory muscle training effects on maximum inspiratory pressure (PImax), heart rate (HR) and HR variability, as well as the quality of life impairment and functionality in patients with Amyotrophic Lateral Sclerosis (ALS). A pilot single-blinded, non-randomized controlled clinical trial was carried out. A total of 20T ALS patients were enrolled and divided into experimental (n = 10) and control (n = 10) groups. The experimental group received POWERbreathe® inspiratory muscle training in conjunction with usual care, and the control group received only usual care for 8 weeks. PImax (measured by POWERbreathe® KH1), HR and HR variability (evaluated by Polar H7), quality of life impairment [measured by the Amyotrophic Lateral Sclerosis Assessment Questionnaire—40 items (ALSAQ-40)] and functionality [assessed by the ALS Functional Rating Scale Revised (ALSFRS-R)] were collected at baseline and after 8 weeks of intervention. We detected statistically significant differences (p < 0.05) with an effect size ranging from medium to large (Cohen’s d = 0.72–1.37); relative to the control group, the experimental group had an increased PImax (mean difference = 10.80 cm H2O; 95% CI = 3.42–18.17) and ALSFRS-R score (mean difference = 5.30 points; 95% CI = −0.03–10.63) and reduced HR (mean difference = −8.80 beats-per-minute; 95% CI = −20.27–2.67) and R-R interval (mean difference = 78.30 ms; 95% CI = 2.89–153.70). POWERbreathe® inspiratory muscle training, in addition to usual care, may improve inspiratory strength and heart rate in patients with ALS. These results encourage larger and longer trials investigating potential clinically relevant benefits of inspiratory muscle training to these patients over the disease course.post-print6421 K

Internalization pathways into cancer cells of gadolinium-based radiosensitizing nanoparticles

International audienceOver the last few decades, nanoparticles have been studied in theranostic field with the objective of exhibiting a long circulation time through the body coupled to major accumulation in tumor tissues, rapid elimination, therapeutic potential and contrast properties. In this context, we developed sub-5 nm gadolinium-based nanoparticles that possess in vitro efficient radiosensitizing effects at moderate concentration when incubated with head and neck squamous cell carcinoma cells (SQ20B). Two main cellular internalization mechanisms were evidenced and quantified: passive diffusion and macropinocytosis. Whereas the amount of particles internalized by passive diffusion is not sufficient to inducein vitro a significant radiosensitizing effect, the cellular uptake by macropinocytosis leads to a successful radiotherapy in a limited range of particles incubation concentration. Macropinocytosis processes in two steps: formation of agglomerates at vicinity of the cell followed by their collect via the lamellipodia (i.e. the "arms") of the cell. The first step is strongly dependent on the physicochemical characteristics of the particles, especially their zeta potential that determines the size of the agglomerates and their distance from the cell. These results should permit to control the quantity of particles internalized in the cell cytoplasm, promising ambitious opportunities towards a particle-assisted radiotherapy using lower radiation doses

The UniProt-GO Annotation database in 2011

The GO annotation dataset provided by the UniProt Consortium (GOA: http://www.ebi.ac.uk/GOA) is a comprehensive set of evidenced-based associations between terms from the Gene Ontology resource and UniProtKB proteins. Currently supplying over 100 million annotations to 11 million proteins in more than 360 000 taxa, this resource has increased 2-fold over the last 2 years and has benefited from a wealth of checks to improve annotation correctness and consistency as well as now supplying a greater information content enabled by GO Consortium annotation format developments. Detailed, manual GO annotations obtained from the curation of peer-reviewed papers are directly contributed by all UniProt curators and supplemented with manual and electronic annotations from 36 model organism and domain-focused scientific resources. The inclusion of high-quality, automatic annotation predictions ensures the UniProt GO annotation dataset supplies functional information to a wide range of proteins, including those from poorly characterized, non-model organism species. UniProt GO annotations are freely available in a range of formats accessible by both file downloads and web-based views. In addition, the introduction of a new, normalized file format in 2010 has made for easier handling of the complete UniProt-GOA data se

The Gene Ontology knowledgebase in 2023

The Gene Ontology (GO) knowledgebase (http://geneontology.org) is a comprehensive resource concerning the functions of genes and gene products (proteins and noncoding RNAs). GO annotations cover genes from organisms across the tree of life as well as viruses, though most gene function knowledge currently derives from experiments carried out in a relatively small number of model organisms. Here, we provide an updated overview of the GO knowledgebase, as well as the efforts of the broad, international consortium of scientists that develops, maintains, and updates the GO knowledgebase. The GO knowledgebase consists of three components: (1) the GO-a computational knowledge structure describing the functional characteristics of genes; (2) GO annotations-evidence-supported statements asserting that a specific gene product has a particular functional characteristic; and (3) GO Causal Activity Models (GO-CAMs)-mechanistic models of molecular "pathways" (GO biological processes) created by linking multiple GO annotations using defined relations. Each of these components is continually expanded, revised, and updated in response to newly published discoveries and receives extensive QA checks, reviews, and user feedback. For each of these components, we provide a description of the current contents, recent developments to keep the knowledgebase up to date with new discoveries, and guidance on how users can best make use of the data that we provide. We conclude with future directions for the project

The SIB Swiss Institute of Bioinformatics' resources: focus on curated databases

The SIB Swiss Institute of Bioinformatics (www.isb-sib.ch) provides world-class bioinformatics databases, software tools, services and training to the international life science community in academia and industry. These solutions allow life scientists to turn the exponentially growing amount of data into knowledge. Here, we provide an overview of SIB's resources and competence areas, with a strong focus on curated databases and SIB's most popular and widely used resources. In particular, SIB's Bioinformatics resource portal ExPASy features over 150 resources, including UniProtKB/Swiss-Prot, ENZYME, PROSITE, neXtProt, STRING, UniCarbKB, SugarBindDB, SwissRegulon, EPD, arrayMap, Bgee, SWISS-MODEL Repository, OMA, OrthoDB and other databases, which are briefly described in this article

Avant-propos

International audienc