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Background Coronavirus Disease 2019 (COVID-19) is a viral pandemic disease that may induce severe pneumonia in humans. In this paper, we investigated the putative implication of 12 vaccines, including BCG, OPV and MMR in the protection against COVID-19. Sequences of the main antigenic proteins in the investigated vaccines and SARS-CoV-2 proteins were compared to identify similar patterns. The immunogenic effect of identified segments was, then, assessed using a combination of structural and antigenicity prediction tools. Results A total of 14 highly similar segments were identified in the investigated vaccines. Structural and antigenicity prediction analysis showed that, among the identified patterns, three segments in Hepatitis B, Tetanus, and Measles proteins presented antigenic properties that can induce putative protective effect against COVID-19. Conclusions Our results suggest a possible protective effect of HBV, Tetanus and Measles vaccines against COVID-19, which may explain the variation of the disease severity among regions.

4 tablas y 4 figuras., A novel strain of the genus Promicromonospora, designated PT9T, was recovered from irradiated roots of the xerophyte Panicum turgidum collected from the Ksar Ghilane oasis in southern Tunisia. Strain PT9T is aerobic, non-spore-forming, Gram- positive actinomycete that produces branched hyphae and forms white to yellowish-white colonies. Chemotaxonomic features, including fatty acids, whole cell sugars and polar lipid profles, support the assignment of PT9T to the genus Promicromonospora. The genomic relatedness indexes based on DNA-DNA hybridization and average nucleotide identity values revealed a signifcant genomic divergence between strain PT9T and all sequenced type strains of the taxon. Phylogenomic analysis showed that isolate PT9T was most closely related to Promicromonospora soli CGMCC 4.7398T. Phenotypic and phylogenomic analyses suggest that isolate PT9T represents a novel species of the genus Promicromonospora, for which the name Promicromonospora panici sp. nov. is proposed. The type strain is PT9T (LMG 31103T= DSM 108613T).The isolate PT9T is an ionizing-radiation-resistant actinobacterium (D10 value=2.6 kGy), with resistance to desiccation and hydrogen peroxide. The complete genome sequence of PT9T consists of 6,582,650 bps with 71.2% G+C content and 6291 protein-coding sequences. This genome will help to decipher the microbial genetic bases for ionizing-radiation resistance mechanisms including the response to oxidative stress., This work was performed under the auspices of Université Lyon 1, CNRS UMR 5557, Écologie Microbienne (France) and the National Center for Nuclear Sciences and Technology CNSTN (Tunisia) and in the ambit of the BIODESERT research program of the LR11-ES31 (BVBGR, ISBST, University of Manouba). The LABGeM (CEA/Genoscope & CNRS UMR8030), the France Génomique and French Bioinformatics Institute national infrastructures (funded as part of Investissement d'Avenir program managed by Agence Nationale pour la Recherche, contracts ANR-10-INBS-09 and ANR-11-INBS-0013) are acknowledged for support within them MicroScope annotation platform.

Although several studies have investigated genetic diversity ofLeishmania infantumin North Africa, genome-wide analyses are lacking. Here, we conducted comparative analyses of nuclear and mitochondrial genomes of sevenL.infantumisolates from Tunisia with the aim to gain insight into factors that drive genomic and phenotypic adaptation. Isolates were from cured (n=4) and recurrent (n=3) visceral leishmaniasis (VL) cases, originating from northern (n=2) and central (n=5) Tunisia, where respectively stable and emerging VL foci are observed. All isolates from relapsed patients were from Kairouan governorate (Centre); one showing resistance to the anti-leishmanial drug Meglumine antimoniate. Nuclear genome diversity of the isolates was analysed by comparison to theL. infantumJPCM5 reference genome. Kinetoplast maxi and minicircle sequences (1 and 59, respectively) were extracted from unmapped reads and identified byblastanalysis against public data sets. The genome variation analysis grouped together isolates from the same geographical origins. Strains from the North were very different from the reference showing more than 34 587 specific single nucleotide variants, with one isolate representing a full genetic hybrid as judged by variant frequency. Composition of minicircle classes within isolates corroborated this geographical population structure. Read depth analysis revealed several significant gene copy number variations correlating with either geographical origin (amastin and Hsp33 genes) or relapse (CLN3 gene). However, no specific gene copy number variation was found in the drug-resistant isolate. In contrast, resistance was associated with a specific minicircle pattern suggestingLeishmaniamitochondrial DNA as a potential novel source for biomarker discovery.

Farming systems include intensive techniques, No-tillage, minimum intervention or organic agriculture. These systems require farmers to have a precise knowledge of agricultural practices. To this, we can add the expertise of new technologies, the control of treatment resistance, the gain of knowledge on seed varieties or the impact on the soil. This mass of information is available on the net: in scientific articles, discussion forums, specialized websites and social networks. It is information in text format, usually unstructured. The objective of this work is to provide an overview of research on textual data mining in agriculture. We present the main methods for extracting relevant information. We test the data mining on data from Scopus, Twitter and a commercial site for agricultural products. We give an example of data classification via machine learning tools. The code to perform this review is on Python.; Les systèmes agricoles vont des techniques intensives aux interventions minimalistes, en passant par le semi-direct. Ces systèmes supposent une connaissance précise des pratiques agricoles par les exploitants et les techniciens. A cela, nous pouvons ajouter la maîtrise des nouvelles technologies, le contrôle des résistances des traitement, l'acquisition des connaissances sur les variétés de semences, l'impact sur les sols, etc. Toute cette masse d'information est disponible sur le net : dans des articles scientifiques, des forums de discussions, des sites web spécialisés et les réseaux sociaux. Ce sont des informations sous format texte, généralement mal structuré. L'objectif de ce travail est de donner une vue générale de la recherche sur la fouille de données textuelles en agriculture. Nous présentons les principales méthodes permettant l'extraction d'informations pertinentes. Nous testons la fouille sur des données de Scopus, de Twitter et d'un site commercial spécialisé en produits agricoles. Nous détaillons un exemple de classification de données via les algorithmes d'apprentissage machine. Le code pour réaliser cette revue est sur Python.

International audience; Phosphogypsum (PG) is an acidic by-product from the phosphate fertilizer industry and it is characterized by a low nutrient availability and the presence of radionuclides and heavy metals which pose a serious problem in its management. Here, we have applied Illumina MiSeq sequencing technology and five bioinformatics pipelines to explore the phylogenetic communities in Tunisian PG. Taking One Codex as a reference method, we present the results of 16S-rDNA-gene-based metataxonomics abundances with four other alternative 2 bioinformatics pipelines (MetaGenome Rapid Annotation using Subsystem Technology (MG RAST), mothur, MICrobial Community Analysis (MICCA) and Quantitative Insights into Microbial Ecology (QIIME)), when analyzing the Tunisian PG. Importantly, based on 16S rDNA datasets, the functional capabilities of microbial communities of PG were deciphered. They suggested the presence of PG autochthonous bacteria recoverable into (1) removal of radioactive elements and toxic heavy metals (2) promotion of plant growth (3) oxidation and (4) reduction of sulfate.

International audience; Computation biology helps to understand processes in organisms from interaction of molecules to complex functions of whole organs. Therefore, there is a need for mathematical methods and models that deliver logical explanations in a reasonable time. We propose herein a method based on algebraic separators, which are special polynomials abundantly studied in effective Galois theory. These polynomials are used in modelling discrete data related to cellular pathways affected in cancer and targeting therapies.

International audience; Phosphogypsum (PG) is an acidic by-product from the phosphate fertilizer industry and it is characterized by a low nutrient availability and the presence of radionuclides and heavy metals which pose a serious problem in its management. Here, we have applied Illumina MiSeq sequencing technology and five bioinformatics pipelines to explore the phylogenetic communities in Tunisian PG. Taking One Codex as a reference method, we present the results of 16S-rDNA-gene-based metataxonomics abundances with four other alternative bioinformatics pipelines (MetaGenome Rapid Annotation using Subsystem Technology (MG-RAST), mothur, MICrobial Community Analysis (MICCA) and Quantitative Insights into Microbial Ecology (QIIME)), when analyzing the Tunisian PG. Importantly, based on 16S rDNA datasets, the functional capabilities of microbial communities of PG were deciphered. They suggested the presence of PG autochthonous bacteria valorizable into (1) removal of radioactive elements and toxic heavy metals, (2) promotion of plant growth, (3) oxidation and (4) reduction of sulfate. These bacteria can be explored further for applications in the bioremediation of by-products, like PG, by different processes.

The aim of the current study is to assess the prevalence ofCampylobacterinfection in broiler chickens, raised in intensive production conditions, and to evaluate the antimicrobial susceptibility of recoveredCampylobacterisolates. A total of 590 cloacal swab samples were taken from 13 broiler chicken flocks in the North East of Tunisia. All samples were tested for the presence of thermophilicCampylobacterby culture and PCR, targeting themapAandceuEgenes, respectively. Susceptibility to antimicrobial drugs was tested against 8 antibiotics. Prevalence ofCampylobacterinfection, relationship with geographic origins and seasons, antimicrobial resistance rates and patterns were analyzed. Total prevalence ofCampylobacterinfection in broiler flocks was in the range of 22.4%, with a predominance ofC. jejuni(68.9%), followed byC. coli(31.1%). Positive association was highlighted between the infection level and the season (P< 0.001), but no link was emphasized considering the geographic origin. Antimicrobial susceptibility testing revealed very high resistance rates detected against macrolide, tetracycline, quinolones, and chloramphenicol, ranging from 88.6% to 100%. Lower resistance prevalence was noticed forβ-lactams (47% and 61.4%) and gentamicin (12.9%). 17 R-type patterns were observed, and a common pattern was found in 30.3% of isolates. This study provides updates and novel data on the prevalence and the AMR of broiler campylobacters in Tunisia, revealing the occurrence of high resistance to several antibiotics and emphasizing the requirement of better surveillance and careful regulation of antimicrobials use.

Computation biology helps to understand all processes in organisms from interaction of molecules to complex functions of whole organs. Therefore, there is a need for mathematical methods and models that deliver logical explanations in a reasonable time. For the last few years there has been a growing interest in biological theory connected to finite fields: the algebraic modeling tools used up to now are based on Gröbner bases or Boolean group. Let n variables representing gene products, changing over the time on p values. A Polynomial dynamical system (PDS) is a function which has several components; each one is a polynom with n variables and coefficient in the finite field Z/pZ that model the evolution of gene products. We propose herein a method using algebraic separators, which are special polynomials abundantly studied in effective Galois theory. This approach avoids heavy calculations and provides a first Polynomial model in linear time.

International audience; Both empirical and theoretical studies, have dealt with the question how to best optimize reproductive fitness for hermaphrodites, using models such as game theory or complicated energetic costs and benefits of mating displays. However, hermaphrodites exhibit a broad spectrum of sexual behaviors like simultaneous, sequential or lifetime gonochorist that cannot be explained using a unique formalism. A possible explanation of this diversity relies on the way these species maximize their fitness: Does the individual hermaphrodite split its time between strategies maximizing its instantaneous reproductive fitness or its evolutionary fitness? Here, we compare these two points of view and extend a game theoretical formalism to a sex allocation model that underlies all sexual behaviors as a result of a dynamic game whose payoff depends on the costs and benefits of sexual reproduction. Using this formalism, we prove that a simultaneous hermaphrodites strategy is stable even for high values of sex changing costs. Moreover, we prove that the stability of a sequential hermaphrodite is linked to the average energy allocated to the pure female strategy.

International audience; A chronic inflammatory state to a large extent explains sickle cell disease (SCD) pathophysi-ology. Nonetheless, the principal dysregulated factors affecting this major pathway and their mechanisms of action still have to be fully identified and elucidated. Integrating gene expression and genome-wide association study (GWAS) data analysis represents a novel approach to refining the identification of key mediators and functions in complex diseases. Here, we performed gene expression meta-analysis of five independent publicly available microarray datasets related to homozygous SS patients with SCD to identify a consensus SCD transcriptomic profile. The meta-analysis conducted using the MetaDE R package based on combining p values (maxP approach) identified 335 differentially expressed genes (DEGs; 224 upregulated and 111 downregulated). Functional gene set enrichment revealed the importance of several metabolic pathways, of innate immune responses, erythrocyte development, and hemostasis pathways. Advanced analyses of GWAS data generated within the framework of this study by means of the atSNP R package and SIFT tool identified 60 regulatory single-nucleotide polymorphisms (rSNPs) occurring in the promoter of 20 DEGs and a deleterious SNP, affecting CAMKK2 protein function. This novel database of candidate genes, transcription factors, and rSNPs associated with SCD provides new markers that may help to identify new therapeutic targets.

Background Hard ticks are hematophagous ectoparasites characterized by their long-term feeding. The saliva that they secrete during their blood meal is their crucial weapon against host-defense systems including hemostasis, inflammation and immunity. The anti-hemostatic, anti-inflammatory and immune-modulatory activities carried out by tick saliva molecules warrant their pharmacological investigation. The Hyalomma dromedarii Koch, 1844 tick is a common parasite of camels and probably the best adapted to deserts of all hard ticks. Like other hard ticks, the salivary glands of this tick may provide a rich source of many compounds whose biological activities interact directly with host system pathways. Female H. dromedarii ticks feed longer than males, thereby taking in more blood. To investigate the differences in feeding behavior as reflected in salivary compounds, we performed de novo assembly and annotation of H. dromedarii sialotranscriptome paying particular attention to variations in gender gene expression. Results The quality-filtered Illumina sequencing reads deriving from a cDNA library of salivary glands led to the assembly of 15,342 transcripts. We deduced that the secreted proteins included: metalloproteases, glycine-rich proteins, mucins, anticoagulants of the mandanin family and lipocalins, among others. Expression analysis revealed differences in the expression of transcripts between male and female H. dromedarii that might explain the blood-feeding strategies employed by both genders. Conclusions The annotated sialome of H. dromedarii helps understand the interaction of tick-host molecules during blood-feeding and can lead to the discovery of new pharmacologically active proteins of ticks of the genus Hyalomma. Electronic supplementary material The online version of this article (10.1186/s13071-018-2874-9) contains supplementary material, which is available to authorized users.

International audience; Leishmania (L.) infantum-infected dogs may present with a large range of clinical signs, from apparently healthy with no or few (asymptomatic dogs, AD) to several clinical signs indicators of active infection (symptomatic dogs, SD). The present study is justified by the conflicting reports describing that either L. infantum-specific IgG1 or IgG2 antibodies may be used as isotype marker of the asymptomatic infection status and by the lack, to our knowledge, of previous analysis of the IgG sub-classes autoantibody repertoires of Leishmania-infected dogs. On the basis of clinical evaluation and laboratory testing (IFAT, parasitological examination of Giemsa-stained lymph node smears, L. infantum antigens-ELISA of total (Tot) IgG), 131 dogs were categorized as SD, asymptomatic seronegative (AND) or seropositive dogs (APD) from surrounding areas, and as negative control dogs (CTD). ELISA based on leishmanial native antigens or recombinant LACK and LeIF proteins showed that SD produce higher levels of specific Tot IgG, IgG1 and IgG2 antibodies than APD, and that for both clinical stages, the antibody titers of IgG2 isotype were constantly higher than those of the IgG1. The seroprevalences of Tot IgG, IgG2 did not differ between APD and SD groups (97 and 97% in SD; 100 and 96% in APD, respectively) whereas that of IgG1 was slightly lower in SD (88% of APD versus 82% of SD). The autoantibody repertoires were analyzed by ELISA using HEp-2 extracts, ds-DNA, human albumin and transferrin as self-antigens and by Western blot using HEp-2 proteins. ELISA results' indicated that APD develop higher levels of IgG1 autoantibodies, and higher seroprevalence (50% and 26% in APD and SD, respectively), contrasting with lower levels and seroprevalences of Tot IgG and IgG2 (43 and 68% for APD; 100 and 74% for SD). Interestingly, SD showed a stronger IgG1 and particularly IgG2 reactivity with transferrin, an iron-binding protein, than APD and AND. Western blotting experiments produced heterogeneous IgG1 and IgG2 inter- and intra-groups reactivity profiles towards HEp-2 proteins, to identify a specific antigenic profile. Generated data from competitive HEp-2-ELISA using leishmanial antigens as inhibitors were in favor that IgG1 antibodies are predominantly autoantibodies to self-antigens in APD whereas they are mainly cross-reactive (Leishmania/self-antigens) in SD.

Le document de ce travail a été publié sur HAL en 2010 (hal-00483257). Le 21 Octobre 2015, un des auteurs, BOUAZIZI Faiçal, a soumis une partie de ce travail sous son seul nom à la revue JAA.La revue JAA (Journal of Algebra and its Applications) l'a publié en ligne le 4 Avril 2017 sous le DOI 10.1142/S021949881850007X mentionné dans les métadonnées de HAL, puis dans ses volumes : Volume 17 N. 1 . 1850007 en 2018.La même année, en 2018, cet article de JAA fit l'objet d'une enquête de la mission intégrité scientifique de l'Université Sorbonne Université :ce document HAL hal-00483257, et une soumission en anglais à une autre revue en 2013 étaient les éléments incontestables qui établirent les faits.Suite aux conclusions indiscutables de cette enquête, la revue JAA a publié en 2019 la correction ci-dessous sur les auteurs effectifs de l'article :https://doi.org/10.1142/S0219498819920014 "Corrigendum: Algebraic certification of numerical algorithms computing Lagrange resolvents"Ines Abdeljaoued-Tej, Faical Bouazizi and Annick Valibouzeaccepté à JAA 12 Décembre 2018, publié 22 Février 2019 voir aussi : https://www.worldscientific.com/doi/abs/10.1142/S0219498819920014?journalCode=jaa; International audience; In this article, we introduce two new methods to calculate Lagrange's resolvents. The first one, based on Lagrange's algorithm, enables to calculate algebraically the resolvent and the second one is numeric with algebraic certification.

The objective of this thesis is to propose an approach for coupling metabolic and ecological levels in a complex biological system. This approach is presented as formal model describing the organism metabolism , which, thanks to DEVS formalism (Discrete Event System Specification), allows a coupling with models of interaction between organisms and between organisms and their environment. A study of the different modeling paradigms allowed us to identify, on the one hand the appropriate paradigm for each level and on the other hand the coupling factors formed by the variables at the interface of individual's internal and external worlds. This coupling explores the effect of lower-level dynamics on the emergence of higher-level characteristics. Two multiagent models, the first on sexual allocation and the second on optimal foraging, concretize the physiology/ecology coupling and show that this coupling makes it possible to connect the individual's internal world with its external world. The strong coupling, in the sense of model integration, explored in a first phase, was improved by the proposal of a formal model, called DEB-DEVS, of the metabolic model (of the Dynamic Energy Budget Theory (DEB)) common to the previous models. This proposal is the result of a reflection on the representation of internal dynamics of agents in ecological models. DEB-DEVS has been illustrated by two classical models of theoretical ecology.; L'objectif de cette thèse est de proposer une approche de couplage des niveaux métabolique et écologique dans un système biologique complexe. Cette approche se présente sous la forme d'un modèle formel décrivant le métabolisme d'un organisme vivant, qui grâce au formalisme DEVS (Discret Event System Specification) adopté, permet un couplage avec des modèles d'interaction entre les organismes et entre l'organisme et son environnement. Une étude des différents paradigmes de modélisation, nous a permis d'identifier d'un côté le paradigme adéquat pour chaque niveau et d'un autre côté les facteurs de couplage formés par les variables à l'interface des mondes internes et externes d'un individu. Ce couplage permet d'explorer l'effet de la dynamique du niveau inférieur sur l'émergence des caractéristiques du niveau supérieur. Deux modèles multi-agents, le premier sur l'allocation sexuelle et le deuxième sur la recherche optimale de nourriture, concrétisent le couplage physiologie/écologie et montrent que ce couplage permet de relier le monde interne de l'individu à son monde externe. Le couplage fort, dans le sens de l'intégration des modèles, exploré dans une première phase, a été amélioré par la proposition d'un modèle formel, nommé DEB-DEVS, du modèle métabolique (de la théorie du budget d'énergie dynamique (DEB)) commun aux modèles précédents. Cette proposition est le résultat d'une réflexion sur la représentation de la dynamique interne des agents dans des modèles de l'écologie. DEB-DEVS a été illustré par deux modèles classiques de l'écologie théorique.

The objective of this thesis is to propose an approach for coupling metabolic and ecological levels in a complex biological system. This approach is presented as formal model describing the organism metabolism , which, thanks to DEVS formalism (Discrete Event System Specification), allows a coupling with models of interaction between organisms and between organisms and their environment.A study of the different modeling paradigms allowed us to identify, on the one hand the appropriate paradigm for each level and on the other hand the coupling factors formed by the variables at the interface of individual's internal and external worlds. This coupling explores the effect of lower-level dynamics on the emergence of higher-level characteristics. Two multiagent models, the first on sexual allocation and the second on optimal foraging, concretize the physiology/ecology coupling and show that this coupling makes it possible to connect the individual's internal world with its external world. The strong coupling, in the sense of model integration, explored in a first phase, was improved by the proposal of a formal model, called DEB-DEVS, of the metabolic model (of the Dynamic Energy Budget Theory (DEB)) common to the previous models. This proposal is the result of a reflection on the representation of internal dynamics of agents in ecological models. DEB-DEVS has been illustrated by two classical models of theoretical ecology.; L'objectif de cette thèse est de proposer une approche de couplage des niveaux métabolique et écologique dans un système biologique complexe. Cette approche se présente sous la forme d'un modèle formel décrivant le métabolisme d'un organisme vivant, qui grâce au formalisme DEVS (Discret event System Specification) adopté, permet un couplage avec des modèles d'interaction entre les organismes et entre l'organisme et son environnement.Une étude des différents paradigmes de modélisation, nous a permis d'identifier d'un côté le paradigme adéquat pour chaque niveau et d'un autre côté les facteurs de couplage formés par les variables à l'interface des mondes internes et externes d'un individu. Ce couplage permet d'explorer l'effet de la dynamique du niveau inférieur sur l'émergence des caractéristiques du niveau supérieur. Deux modèles multi-agents, le premier sur l'allocation sexuelle et le deuxième sur la recherche optimale de nourriture, concrétisent le couplage physiologie/écologie et montrent que ce couplage permet de relier le monde interne de l'individu à son monde externe. Le couplage fort, dans le sens de l'intégration des modèles, exploré dans une première phase, a été amélioré par la proposition d'un modèle formel, nommé DEB-DEVS, du modèle métabolique (de la théorie du budget d'énergie dynamique (DEB)) commun aux modèles précédents. Cette proposition est le résultat d'une réflexion sur la représentation de la dynamique interne des agents dans des modèles de l'écologie. DEB-DEVS a été illustré par deux modèles classiques de l'écologie théorique.

International audience; Genus Oenothera includes medicinal plants that are distributed throughout the world and are known since ancient times. Popular indications of different species of this genus include treatment of inflammations, diabetes, microbial infections, ulcers, tumors, kidney and liver problems. The plants of this genus are a botanical source for various pharmaceutically active components like sterols, alkaloids, phenolic acids, flavonoids, triterpe-noids, saponins, biflavonols and tocopherols. This review article is a compilation of chemical composition and biological activities of the various species of the genus Oenothera.

International audience; BLB406 is a novel isolate of Bacillus thuringiensis with a larvicidal activity against Aedes aegypti larvae. It displays original plasmidic and crystal protein patterns. The present work reported molecular and bioinformatic analyses for the genome sequence of BLB406 using MiSeq Illumina next-generation sequencing technology. The reads were assembled by Velvet tool. Using RAST program and PGAAP, the genome of BLB406 strain was shown to contain 6297 genes corresponding to 5924 protein coding sequences. The BLB406 genome investigation with BtToxin_scanner program shows that this strain has an original and different combination of toxins compared to the published ones: five cry genes (cry11, cry22, cry2, cry60, cry64) and two distinct vegetative insecticidal vip4 genes. This combination provides a potential larvicidal and anti-cancer activities to BLB406. It might be a potential solution to some problems such as the narrow insecticidal spectra and insect resistance. The whole BLB406 genome information provides a valuable background for future in silico analyses as well as biotechnological applications in order to increase the production of commercial bioinsecticide based on BLB406 B. thuringiensis strain.

International audience; Background. Olive oils (OOs) show high chemical variability due to several factors of genetic, environmental and anthropic types. Genetic and environmental factors are responsible for natural compositions and polymorphic diversification resulting in different varietal patterns and phenotypes. Anthropic factors, however, are at the origin of different blends' preparation leading to normative, labelled or adulterated commercial products. Control of complex OO samples requires their (i) characterization by specific markers; (ii) authentication by fingerprint patterns; and (iii) monitoring by traceability analysis.Methods. These quality control and management aims require the use of several multivariate statistical tools: specificity highlighting requires ordination methods; authentication checking calls for classification and pattern recognition methods; traceability analysis implies the use of network-based approaches able to separate or extract mixed information and memorized signals from complex matrices. Results. This chapter presents a review of different chemometrics methods applied for the control of OO variability from metabolic and physical-chemical measured characteristics. The different chemometrics methods are illustrated by different study cases on monovarietal and blended OO originated from different countries.Conclusion. Chemometrics tools offer multiple ways for quantitative evaluations and qualitative control of complex chemical variability of OO in relation to several intrinsic and extrinsic factors.

International audience; Olive oil blends (OOBs) are complex matrices combining different cultivars at variable proportions. Although qualitative determinations of OOBs have been subjected to several chemometric works, quantitative evaluations of their contents remain poorly developed because of traceability difficulties concerning co-occurring cultivars. Around this question, we recently published an original simplex approach helping to develop predictive models of the proportions of co-occurring cultivars from chemical profiles of resulting blends (Semmar & Artaud, 2015). Beyond predictive model construction and validation, this paper presents an extension based on prediction errors' analysis to statistically define the blends with the highest predictability among all the possible ones that can be made by mixing cultivars at different proportions. This provides an interesting way to identify a priori labeled commercial products with potentially high traceability taking into account the natural chemical variability of different constitutive cultivars.

Le document de ce travail a été publié sur HAL en 2010 (hal-00483257). Le 21 Octobre 2015, un des auteurs, BOUAZIZI Faiçal, a soumis une partie de ce travail sous son seul nom à la revue JAA.La revue JAA (Journal of Algebra and its Applications) l'a publié en ligne le 4 Avril 2017 sous le DOI 10.1142/S021949881850007X mentionné dans les métadonnées de HAL, puis dans ses volumes : Volume 17 N. 1 . 1850007 en 2018.La même année, en 2018, cet article de JAA fit l'objet d'une enquête de la mission intégrité scientifique de l'Université Sorbonne Université :ce document HAL hal-00483257, et une soumission en anglais à une autre revue en 2013 étaient les éléments incontestables qui établirent les faits.Suite aux conclusions indiscutables de cette enquête, la revue JAA a publié en 2019 la correction ci-dessous sur les auteurs effectifs de l'article :https://doi.org/10.1142/S0219498819920014 "Corrigendum: Algebraic certification of numerical algorithms computing Lagrange resolvents"Ines Abdeljaoued-Tej, Faical Bouazizi and Annick Valibouzeaccepté à JAA 12 Décembre 2018, publié 22 Février 2019 voir aussi : https://www.worldscientific.com/doi/abs/10.1142/S0219498819920014?journalCode=jaa; International audience; In this article, we introduce two new methods to calculate Lagrange's resolvents. The first one, based on Lagrange's algorithm, enables to calculate algebraically the resolvent and the second one is numeric with algebraic certification.

Background: Although pockets of bioinformatics excellence have developed in Africa, generally, large-scale genomic data analysis has been limited by the availability of expertise and infrastructure. H3ABioNet, a pan-African bioinformatics network, was established to build capacity specifically to enable H3Africa (Human Heredity and Health in Africa) researchers to analyze their data in Africa. Since the inception of the H3Africa initiative, H3ABioNet’s role has evolved in response to changing needs from the consortium and the African bioinformatics community.Objectives: H3ABioNet set out to develop core bioinformatics infrastructure and capacity for genomics research in various aspects of data collection, transfer, storage, and analysis.Methods and Results: Various resources have been developed to address genomic data management and analysis needs of H3Africa researchers and other scientific communities on the continent. NetMap was developed and used to build an accurate picture of network performance within Africa and between Africa and the rest of the world, and Globus Online has been rolled out to facilitate data transfer. A participant recruitment database was developed to monitor participant enrollment, and data is being harmonized through the use of ontologies and controlled vocabularies. The standardized metadata will be integrated to provide a search facility for H3Africa data and biospecimens. Because H3Africa projects are generating large-scale genomic data, facilities for analysis and interpretation are critical. H3ABioNet is implementing several data analysis platforms that provide a large range of bioinformatics tools or workflows, such as Galaxy, the Job Management System, and eBiokits. A set of reproducible, portable, and cloud-scalable pipelines to support the multiple H3Africa data types are also being developed and dockerized to enable execution on multiple computing infrastructures. In addition, new tools have been developed for analysis of the uniquely divergent African data and for downstream interpretation of prioritized variants. To provide support for these and other bioinformatics queries, an online bioinformatics helpdesk backed by broad consortium expertise has been established. Further support is provided by means of various modes of bioinformatics training.Conclusions: For the past 4 years, the development of infrastructure support and human capacity through H3ABioNet, have significantly contributed to the establishment of African scientific networks, data analysis facilities, and training programs. Here, we describe the infrastructure and how it has affected genomics and bioinformatics research in Africa.HighlightsH3ABioNet is building capacity to enable analysis of genomic data in Africa.Infrastructure has been built for clinical and genomic data storage, management, and analysis.New algorithms and pipelines for African genomic data analysis have been developed.Data are being harmonized using ontologies to enable easy search and retrieval.Genomics training is implemented using various online and face-to-face approaches.

Background Leishmania (L) are intracellular protozoan parasites that are able to survive and replicate within the harsh and potentially hostile phagolysosomal environment of mammalian mononuclear phagocytes. A complex interplay then takes place between the macrophage (MΦ) striving to eliminate the pathogen and the parasite struggling for its own survival. To investigate this host-parasite conflict at the transcriptional level, in the context of monocyte-derived human MΦs (MDM) infection by L. major metacyclic promastigotes, the quantitative technique of serial analysis of gene expression (SAGE) was used. Results After extracting mRNA from resting human MΦs, Leishmania-infected human MΦs and L. major parasites, three SAGE libraries were constructed and sequenced generating up to 28,173; 57,514 and 33,906 tags respectively (corresponding to 12,946; 23,442 and 9,530 unique tags). Using computational data analysis and direct comparison to 357,888 publicly available experimental human tags, the parasite and the host cell transcriptomes were then simultaneously characterized from the mixed cellular extract, confidently discriminating host from parasite transcripts. This procedure led us to reliably assign 3,814 tags to MΦs' and 3,666 tags to L. major parasites transcripts. We focused on these, showing significant changes in their expression that are likely to be relevant to the pathogenesis of parasite infection: (i) human MΦs genes, belonging to key immune response proteins (e.g., IFNγ pathway, S100 and chemokine families) and (ii) a group of Leishmania genes showing a preferential expression at the parasite's intra-cellular developing stage. Conclusion Dual SAGE transcriptome analysis provided a useful, powerful and accurate approach to discriminating genes of human or parasitic origin in Leishmania-infected human MΦs. The findings presented in this work suggest that the Leishmania parasite modulates key transcripts in human MΦs that may be beneficial for its establishment and survival. Furthermore, these results provide an overview of gene expression at two developmental stages of the parasite, namely metacyclic promastigotes and intracellular amastigotes and indicate a broad difference between their transcriptomic profiles. Finally, our reported set of expressed genes will be useful in future rounds of data mining and gene annotation.