A Generic API for Load Balancing in Structured P2P Systems

International audienceReal world datasets are known to be highly skewed, often leading to an important load imbalance issue for distributed systems managing them. To address this issue, there exist almost as many load balancing strategies as there are different systems. When designing a scalable distributed system geared towards handling large amounts of information, it is often not so easy to anticipate which kind of strategy will be the most efficient to maintain adequate performance regarding response time, scalability and reliability at any time. Based on this observation, we describe the methodology behind the building of a generic API to implement and experiment any strategy independently from the rest of the code, prior to a definitive choice for instance. We then show how this API is compatible with famous existing systems and their load balancing scheme. We also present results from our own distributed system which targets the continuous storage of events structured according to the Semantic Web standards, further retrieved by interested parties. As such, our system constitutes a typical example of a Big Data environment

Évaluation d'une architecture de stockage RDF distribuée

Atelier "Ontologies et Jeux de Données pour évaluer le web sémantique (OJD)"Stocker des informations du web sémantique implique d'être capable de pouvoir potentiellement gérer de très importants volumes de données. D'où le besoin d'opter pour une solution forcément distribuée, entre autres de type pair-à-pair, pour pouvoir passer à l'échelle. Un système de stockage RDF réparti requiert de mettre en place un algorithme particulier pour la résolution des requêtes SPARQL. Les données étant distribuées à travers un réseau de pairs, il est nécessaire d'exécuter une partie de la requête sur certains de ces pairs, puis d'agréger et d'appliquer d'éventuelles conditions de filtrage sur les différents résultats intermédiaires obtenus, avant de pouvoir retourner les résultats finaux. Il existe actuellement une douzaine de benchmarks pour le RDF, mais aucun d'entre eux ne se présente comme étant pensé pour s'adapter à une architecture de stockage réparti. Dans cet article, nous mettons en évidence le nombre de résultats intermédiaires générés par les requêtes SPARQL, un aspect important dans un contexte distribué, et qui nous semble à l'heure actuelle négligé par les benchmarks pour le RDF

Molecular prevalence, genetic characterization and patterns of Toxoplasma gondii infection in domestic small mammals from Cotonou, Benin

Toxoplasmosis, one of the most prevalent parasitic infections in humans and animals, is caused by the intracellular protozoan parasite Toxoplasma gondii. Small mammals play a key role as intermediate reservoir hosts in the maintenance of the T. gondii life cycle. In this study, we estimated the molecular prevalence and provide genetic diversity data for T. gondii in 632 small mammals sampled in four areas of Cotonou city, Benin. Both the brain and heart of each individual were screened through T. gondii-targeting qPCR, and positive samples were then genotyped using a set of 15 T. gondii-specific microsatellites. Prevalence data were statistically analyzed in order to assess the relative impact of individual host characteristics, spatial distribution, composition of small mammal community, and urban landscape features. An overall T. gondii molecular prevalence of 15.2% was found and seven genotypes, all belonging to the Africa 1 lineage, could be retrieved from the invasive black rat Rattus rattus and the native African giant shrew Crocidura olivieri. Statistical analyses did not suggest any significant influence of the environmental parameters used in this study. Rather, depending on the local context, T. gondii prevalence appeared to be associated either with black rat, shrew, or mouse abundance or with the trapping period. Overall, our results highlight the intricate relationships between biotic and abiotic factors involved in T. gondii epidemiology and suggest that R. rattus and C. olivieri are two competent reservoirs for the Africa 1 lineage, a widespread lineage in tropical Africa and the predominant lineage in Benin

Copernicus Ocean State Report, issue 6

The 6th issue of the Copernicus OSR incorporates a large range of topics for the blue, white and green ocean for all European regional seas, and the global ocean over 1993–2020 with a special focus on 2020

Obeticholic acid for the treatment of non-alcoholic steatohepatitis: interim analysis from a multicentre, randomised, placebo-controlled phase 3 trial

Background Non-alcoholic steatohepatitis (NASH) is a common type of chronic liver disease that can lead to cirrhosis. Obeticholic acid, a farnesoid X receptor agonist, has been shown to improve the histological features of NASH. Here we report results from a planned interim analysis of an ongoing, phase 3 study of obeticholic acid for NASH. Methods In this multicentre, randomised, double-blind, placebo-controlled study, adult patients with definite NASH,non-alcoholic fatty liver disease (NAFLD) activity score of at least 4, and fibrosis stages F2–F3, or F1 with at least oneaccompanying comorbidity, were randomly assigned using an interactive web response system in a 1:1:1 ratio to receive oral placebo, obeticholic acid 10 mg, or obeticholic acid 25 mg daily. Patients were excluded if cirrhosis, other chronic liver disease, elevated alcohol consumption, or confounding conditions were present. The primary endpointsfor the month-18 interim analysis were fibrosis improvement (≥1 stage) with no worsening of NASH, or NASH resolution with no worsening of fibrosis, with the study considered successful if either primary endpoint was met. Primary analyses were done by intention to treat, in patients with fibrosis stage F2–F3 who received at least one dose of treatment and reached, or would have reached, the month 18 visit by the prespecified interim analysis cutoff date. The study also evaluated other histological and biochemical markers of NASH and fibrosis, and safety. This study is ongoing, and registered with ClinicalTrials.gov, NCT02548351, and EudraCT, 20150-025601-6. Findings Between Dec 9, 2015, and Oct 26, 2018, 1968 patients with stage F1–F3 fibrosis were enrolled and received at least one dose of study treatment; 931 patients with stage F2–F3 fibrosis were included in the primary analysis (311 in the placebo group, 312 in the obeticholic acid 10 mg group, and 308 in the obeticholic acid 25 mg group). The fibrosis improvement endpoint was achieved by 37 (12%) patients in the placebo group, 55 (18%) in the obeticholic acid 10 mg group (p=0·045), and 71 (23%) in the obeticholic acid 25 mg group (p=0·0002). The NASH resolution endpoint was not met (25 [8%] patients in the placebo group, 35 [11%] in the obeticholic acid 10 mg group [p=0·18], and 36 [12%] in the obeticholic acid 25 mg group [p=0·13]). In the safety population (1968 patients with fibrosis stages F1–F3), the most common adverse event was pruritus (123 [19%] in the placebo group, 183 [28%] in the obeticholic acid 10 mg group, and 336 [51%] in the obeticholic acid 25 mg group); incidence was generally mild to moderate in severity. The overall safety profile was similar to that in previous studies, and incidence of serious adverse events was similar across treatment groups (75 [11%] patients in the placebo group, 72 [11%] in the obeticholic acid 10 mg group, and 93 [14%] in the obeticholic acid 25 mg group). Interpretation Obeticholic acid 25 mg significantly improved fibrosis and key components of NASH disease activity among patients with NASH. The results from this planned interim analysis show clinically significant histological improvement that is reasonably likely to predict clinical benefit. This study is ongoing to assess clinical outcomes

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

Contacts et acculturations en Méditerranée occidentale

La question des contacts entre les différents peuples qui bordent les rives de la Méditerranée nord occidentale est l’un des sujets phares de la recherche archéologique de ces trente dernières années. Que l’on parle d’époque archaïque et classique ou de Protohistoire et d’âge du Fer, les échanges et les processus d’acculturation de ces peuples qui entrèrent alors en contact les uns avec les autres : Grecs, Celtes, Phéniciens, Ibères, Ligures, Étrusques, ont retenu l’attention des chercheurs travaillant sur l’expansion grecque dans ces régions, sur les trafics commerciaux, sur les échanges culturels. L’œuvre de Michel Bats (Directeur de recherche honoraire du CNRS) traverse toutes ces thématiques : la présence des Phocéens et des Étrusques dans le bassin occidental de la Méditerranée, l’acculturation et les identités ethno-culturelles, les recherches sur la céramique et ses usages dans une perspective anthropologique, l’appropriation de l’écriture par les sociétés protohistoriques. Ses collègues et amis, en organisant ce colloque et en participant à ces actes, entendent lui témoigner leur amitié et leur dette intellectuelle. Ce volume réunit des articles des meilleurs spécialistes, actuels de la question - des chercheurs de toute la Méditerranée - autour des quatre grands thèmes que nous venons d’évoquer afin tout à la fois de dresser un bilan et de définir de nouvelles perspectives. Cet ouvrage présente donc aussi bien des synthèses - sur la présence grecque en Espagne, sur l’origine de l’écriture, sur les pratiques funéraires, sur les identités culturelles et ethniques - que des découvertes récentes concernant la thématique des contacts et de l’acculturation en Méditerranée nord occidentale : l’agglomération du Premier âge du Fer de La Cougourlude (Lattes, Hérault) fouillée durant l’été 2010 ; le sanctuaire hellénistique de Cumes et les fouilles récentes de Fratte en Italie ; les ateliers de potiers de Rosas en Espagne ; les dernières découvertes d’Olbia de Provence

Extracorporeal Membrane Oxygenation for Severe Acute Respiratory Distress Syndrome associated with COVID-19: An Emulated Target Trial Analysis.

RATIONALE: Whether COVID patients may benefit from extracorporeal membrane oxygenation (ECMO) compared with conventional invasive mechanical ventilation (IMV) remains unknown. OBJECTIVES: To estimate the effect of ECMO on 90-Day mortality vs IMV only Methods: Among 4,244 critically ill adult patients with COVID-19 included in a multicenter cohort study, we emulated a target trial comparing the treatment strategies of initiating ECMO vs. no ECMO within 7 days of IMV in patients with severe acute respiratory distress syndrome (PaO2/FiO2 <80 or PaCO2 ≥60 mmHg). We controlled for confounding using a multivariable Cox model based on predefined variables. MAIN RESULTS: 1,235 patients met the full eligibility criteria for the emulated trial, among whom 164 patients initiated ECMO. The ECMO strategy had a higher survival probability at Day-7 from the onset of eligibility criteria (87% vs 83%, risk difference: 4%, 95% CI 0;9%) which decreased during follow-up (survival at Day-90: 63% vs 65%, risk difference: -2%, 95% CI -10;5%). However, ECMO was associated with higher survival when performed in high-volume ECMO centers or in regions where a specific ECMO network organization was set up to handle high demand, and when initiated within the first 4 days of MV and in profoundly hypoxemic patients. CONCLUSIONS: In an emulated trial based on a nationwide COVID-19 cohort, we found differential survival over time of an ECMO compared with a no-ECMO strategy. However, ECMO was consistently associated with better outcomes when performed in high-volume centers and in regions with ECMO capacities specifically organized to handle high demand. This article is open access and distributed under the terms of the Creative Commons Attribution Non-Commercial No Derivatives License 4.0 (http://creativecommons.org/licenses/by-nc-nd/4.0/)

Improving skewed data dissemination in structured overlays

De nombreux systèmes distribués sont confrontés au problème du déséquilibre de charge entre machines. Avec l'émergence du Big Data, de larges volumes de données aux valeurs souvent biaisées sont produits par des sources hétérogènes pour être souvent traités en temps réel. Il faut donc être capable de s'adapter aux variations de volume/contenu/provenance de ces données. Nous nous intéressons ici aux données RDF, un format du Web Sémantique. Nous proposons une nouvelle approche pour améliorer la répartition des données, basée sur l'utilisation de plusieurs fonctions de hachage préservant l'ordre naturel des données dans le réseau. Cela permet à chaque pair de pouvoir indépendamment modifier la fonction de hachage qu'il applique sur les données afin de réduire l'intervalle de valeurs dont il est responsable. Plus généralement, pour résoudre le problème du déséquilibre de charge, il existe presque autant de stratégies qu'il y a de systèmes différents. Nous montrons que de nombreux dispositifs d'équilibrage de charge sont constitués des mêmes éléments de base, et que seules la mise en œuvre et l'interconnexion de ces éléments varient. Partant de ce constat, nous décrivons les concepts derrière la construction d'une API générique pour appliquer une stratégie d'équilibrage de charge qui est indépendante du reste du code. Mise en place sur notre système, l'API a un impact minimal sur le code métier et permet de changer une partie d'une stratégie sans modifier d'autres composants. Nous montrons aussi que la variation de certains paramètres peut influer sur les résultats obtenus.Many distributed systems face the problem of load imbalance between machines. With the advent of Big Data, large datasets whose values are often highly skewed are produced by heterogeneous sources to be often processed in real time. Thus, it is necessary to be able to adapt to the variations of size/content/source of the incoming data. In this thesis, we focus on RDF data, a format of the Semantic Web. We propose a novel approach to improve data distribution, based on the use of several order-preserving hash functions. This allows an overloaded peer to independently modify its hash function in order to reduce the interval of values it is responsible for. More generally, to address the load imbalance issue, there exist almost as many load balancing strategies as there are different systems. We show that many load balancing schemes are comprised of the same basic elements, and only the implementation and interconnection of these elements vary. Based on this observation, we describe the concepts behind the building of a common API to implement any load balancing strategy independently from the rest of the code. Implemented on our distributed storage system, the API has a minimal impact on the business code and allows the developer to change only a part of a strategy without modifying the other components. We also show how modifying some parameters can lead to significant improvements in terms of results