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EMULSION: Transparent and flexible multiscale stochastic models in human, animal and plant epidemiology
No full textStochastic mechanistic epidemiological models largely contribute to better understand pathogen emergence and spread, and assess control strategies at various scales (from within-host to transnational scale). However, developing realistic models which involve multi-disciplinary knowledge integration faces three major challenges in predictive epidemiology: lack of readability once translated into simulation code, low reproducibility and reusability, and long development time compared to outbreak time scale. We introduce here EMULSION, an artificial intelligence-based software intended to address those issues and help modellers focus on model design rather than programming. EMULSION defines a domain-specific language to make all components of an epidemiological model (structure, processes, parameters…) explicit as a structured text file. This file is readable by scientists from other fields (epidemiologists, biologists, economists), who can contribute to validate or revise assumptions at any stage of model development. It is then automatically processed by EMULSION generic simulation engine, preventing any discrepancy between model description and implementation. The modelling language and simulation architecture both rely on the combination of advanced artificial intelligence methods (knowledge representation and multi-level agent-based simulation), allowing several modelling paradigms (from compartment- to individual-based models) at several scales (up to metapopulation). The flexibility of EMULSION and its capability to support iterative modelling are illustrated here through examples of progressive complexity, including late revisions of core model assumptions. EMULSION is also currently used to model the spread of several diseases in real pathosystems. EMULSION provides a command-line tool for checking models, producing model diagrams, running simulations, and plotting outputs. Written in Python 3, EMULSION runs on Linux, MacOS, and Windows. It is released under Apache-2.0 license. A comprehensive documentation with installation instructions, a tutorial and many examples are available from: https://sourcesup.renater.fr/www/emulsion-public
Pistacia atlantica desf., a source of healthy vegetable oil
No full textPistacia atlantica, which belongs to the Anacardiaceae family, is an important species for rural people in arid and semi-arid areas. The fruit, rich in oil, is used in traditional medicine for the treatment of various diseases. The oil extracted from this species growing in a northern area of Algeria and its fatty acid composition were previously studied. However, the largest areas where this species is present (traditional cultivation) is located in southern Algeria. Moreover, studies on oil fatty acid composition and essential oil were always conducted separately. This study was performed in order to assess the fatty acid and volatile organic compound composition of P. atlantica vegetable oil. The seeds were collected randomly from Djelfa (300 km South of Algiers, Algeria). Oil content and fatty acid composition were determined by Soxhlet extraction. The seeds contained high concentrations of oil (32-67%). The major fatty acids were oleic (39-49%), linoleic (23.6-31%), and palmitic (21.3-26.6%) acids. The ratio of polyunsaturated fatty acids (PUFA) to saturated fatty acids (SFA) indicated that the content of unsaturated fatty acids was approximately three times higher than that of SFA. This ratio is widely used in epidemiological studies and research on cardiovascular diseases, diabetes, and metabolic syndrome. The ratios of omega-acids, i.e., omega-9/omega-6 and omega-6/omega-3, were 1.3-2 and 18.5-38.3, respectively. Crushed seeds were analyzed by headspace solid-phase microextraction (SPME) coupled with gas chromatography-mass spectrometry. More than 40 compounds were identified, mainly monoterpenes (C10H16), such as alpha-terpinene and terpinolene, but also sesquiterpenes (C15H24) at lower levels. The value of this species as a source of healthy oil rich in omega-3 acid and its effects on cardiovascular disease risk are discussed
Influence of sampling design parameters on biomass predictions derived from airborne LiDAR data
No full textThis study investigated the influence of sampling design parameters on biomass prediction accuracy obtained from airborne lidar data. A one-factor-at-a-time and a global sensitivity analyses were applied to identify the parameters most impacting model accuracy. We focused on several lidar and field survey parameters that can be easily controlled by users. In this pine plantations study site, a decrease in pulse density (4 to 0.5 pulse/m(2)) led to a small decrease in prediction accuracy (?3%). However, variability in the number of field plots, positioning accuracy, and plot size, significantly impacted model performance. To obtain a robust model, a minimum of 40 field plots, along with field plot position accuracy of 5?m or lower, and field plot radius exceeding 13?m are recommended. The minimum diameter at breast height (DBH) threshold and the choice of the allometric biomass equation were found to have lesser impacts on model accuracy. In addition, accuracies of DBH and tree height measurements were respectively shown to have a minor and negligible contribution to the prediction error. Significant field measurement costs will still be needed to ensure good-quality models for biomass mapping. However, by reducing pulse density, cost savings can be made on lidar acquisition.Cette étude a examiné l'influence de différents paramètres sur l’estimation de la biomasse à partir de données de lidar aéroportés. Une approche consistant à faire varier les paramètres indépendamment les uns des autres et une analyse de sensibilité globale ont été utilisées pour identifier les paramètres ayant le plus d’impact sur la précision des modèles. Nous nous sommes concentrés sur plusieurs paramètres relatifs aux acquisitions lidar et aux inventaires de terrain qui peuvent être facilement contrôlées. Sur notre site d'étude, composé de plantations de pins, une diminution de la densité d'impulsions lidar (4 à 0,5 impulsions/m2) a conduit à une légère diminution de la précision de l’estimation (−3%). Cependant, la variabilité du nombre de placettes inventoriées, la précision de positionnement et la taille des placettes, impactent de manière significative la performance du modèle. Pour obtenir un modèle robuste, un minimum de 40 placettes inventoriées, un positionnement précis des placettes de 5 m ou moins, ainsi que des placettes inventoriées sur un rayon supérieur à 13 m sont recommandés. Le seuil de recensabilité des arbres ainsi que le choix de l'équation allométrique se sont avérés avoir un impact moindre sur la précision des modèles. De plus, les précisions sur la mesure du diamètre à hauteur de poitrine et sur celle de la hauteur des arbres ne représentent respectivement qu’une contribution mineure et négligeable à l'erreur commise sur l’estimation de la biomasse. Les coûts relatifs aux inventaires de terrain devront encore rester significatifs pour assurer des modèles lidar de qualité. Cependant, en réduisant la densité d'impulsion, des économies peuvent être faites lors du survol lidar
Accumulation of intramuscular toxic lipids, a link between fat mass accumulation and sarcopenia
No full textAging is characterized by a loss in muscle mass and function, which is defined as sarcopenia. It weakens individuals by increasing the risk of falls and altering their quality of life. The loss of muscle mass results from the age-related impairment of the anabolic effect of nutrients and insulin, which normally increase and decrease muscle protein synthesis and degradation rates respectively. Alterations in muscle protein metabolism have been related to the accumulation of body fat and intramyocellular lipids. In particular, some lipid species such as ceramides or diacylglycerols have been described as inhibitors of the insulin signaling pathway in different models. Accumulation of these molecules in skeletal muscle could result from a lowered buffering capacity of circulating fatty acids by adipose tissue in response to the meal, a reduction of mitochondrial oxidative capacities or chronic inflammation. However, some nutritional strategies have been identified to limit or prevent the accumulation of lipotoxic metabolites and to improve the sensitivity of muscle to nutrients or insulin
Evaluation of 23 gridded precipitation datasets across West Africa
No full textThis study aims reporting on 23 gridded precipitation datasets (P-datasets) reliability across West
Africa through direct comparisons with rain gauges measurement at the daily and monthly time scales
over a 4 years period (2000-2003). All P-datasets reliability vary in space and time. The most efficient
P-dataset in term of Kling–Gupta Efficiency (KGE) changes at the local scale and the P-dataset
performance is sensitive to seasonal effects. Satellite-based P-datasets performed better during the
wet than the dry season whereas the opposite is observed for reanalysis P-datasets. The best overall
performance was obtained for MSWEP v.2.2 and CHIRPS v.2 for daily and monthly time-step,
respectively. Part of the differences in P-dataset performance at daily and monthly time step comes
from the time step used to proceed the gauges adjustment (i.e day or month) and from a mismatch
between gauge and satellite reporting times. In comparison to the others P-datasets, TMPA-Adj v.7
reliability is stable and reach the second highest KGE value at both daily and monthly time step.
Reanalysis P-datasets (WFDEI, MERRA-2, JRA-55, ERA-Interim) present among the lowest statistical
scores at the daily time step, which drastically increased at the monthly time step for WFDEI and
MERRA-2. The non-adjusted P-datasets were the less efficient, but, their near-real time availability
should be helpful for risk forecast studies (i.e. GSMaP-RT v.6). The results of this study give important
elements to select the most adapted P-dataset for specific application across West Africa
Ecological conditions and molecular determinants involved in agrobacterium lifestyle in tumors
No full textThe study of pathogenic agents in their natural niches allows for a better understanding of disease persistence and dissemination. Bacteria belonging to the Agrobacterium genus are soil-borne and can colonize the rhizosphere. These bacteria are also well known as phytopathogens as they can cause tumors (crown gall disease) by transferring a DNA region (T-DNA) into a wide range of plants. Most reviews on Agrobacterium are focused on virulence determinants, T-DNA integration, bacterial and plant factors influencing the efficiency of genetic transformation. Recent research papers have focused on the plant tumor environment on the one hand, and genetic traits potentially involved in bacterium-plant interactions on the other hand. The present review gathers current knowledge about the special conditions encountered in the tumor environment along with the Agrobacterium genetic determinants putatively involved in bacterial persistence inside a tumor. By integrating recent metabolomic and transcriptomic studies, we describe how tumors develop and how Agrobacterium can maintain itself in this nutrient-rich but stressful and competitive environment
Effects of nutrient intake during pregnancy and lactation on the endocrine pancreas of the offspring
No full textThe pancreas has an essential role in the regulation of glucose homeostasis by secreting insulin, the only hormone with a blood glucose lowering effect in mammals. Several circulating molecules are able to positively or negatively influence insulin secretion. Among them, nutrients such as fatty acids or amino acids can directly act on specific receptors present on pancreatic beta cells. Dietary intake, especially excessive nutrient intake, is known to modify energy balance in adults, resulting in pancreatic dysfunction. However, gestation and lactation are critical periods for fetal development and pup growth and specific dietary nutrients are required for optimal growth. Feeding alterations during these periods will impact offspring development and increase the risk of developing metabolic disorders in adulthood, leading to metabolic programming. This review will focus on the influence of nutrient intake during gestation and lactation periods on pancreas development and function in offspring, highlighting the molecular mechanism of imprinting on this organ
Influence de la texture des aliments sur la digestion des macronutriments et la libération de micronutriments: étude in vitro sur masticateur et digesteur dynamique paramétrés à partir de données in vivo
No full textIntroduction et but de l’étude: Dans les années à venir, un des défis majeurs de l’optimisation nutritionnelle consistera à lutter contre les carences en micronutriments. Une des stratégies couramment utilisée pour cela est l’enrichissement des aliments, mais sa pertinence reste à prouver au regard de son efficacité réelle. Alors que les caractéristiques structurales des aliments influencent le processus de désintégration pendant la digestion, il semble pertinent d'évaluer l'impact de la structure des aliments sur la biodisponibilité des micronutriments.Matériel et méthodes: Trois aliments enrichis en lutéine et vitamine D ont été conçus à composition strictement identique (sur matière sèche) mais avec des structures et textures différentes (crème anglaise, génoise et biscuit). Lors d’une étude préliminaire in vivochez l’Homme, les caractéristiques des bols alimentaires produits à partir de ces matrices et leurs cinétiques de digestion avaient été étudiées. Après reproduction des bols alimentaires à l’identique des bols in vivopar le simulateur de mastication AM², ceux-ci ont été soumis à une digestion in vitroà l’aide du simulateur de digestion dynamique DIDGI (n=3). Les cinétiques de désintégration de la matrice (protéolyse, lipolyse et amylolyse) et la libération des micronutriments dans la phase soluble (marqueur de la bioaccessibilité) ont été suivies. UneAnalyse en Composantes Principales a ensuite permis de déterminer les corrélations entre variables.[br/]
Résultats et Analyse statistique: Les cinétiques de désintégration de la matrice sont influencées par l’aliment, en particulier en ce qui concerne la destruction du réseau amylacé: elle est ainsi significativement plus faible pour le biscuit par rapport aux deux autres matrices. En outre, des différences en termes de lipolyse et d’amylolyse ont été observées. Le biscuit montre ainsi une libération d’acidesgras libres et d’oligosaccharides significativement plus faible que les deux autres matrices en phase intestinale de digestion, la génoise présentant quant à elle les valeurs les plus élevées. La structure de la matrice ne semble toutefoisavoir aucun effet sur la protéolyse.Les cinétiques de libération des micronutriments sont également distinctes mais les tendances ne sont pas les mêmes selon le micronutriment considéré. En phase gastrique, les différences entre matrices sont peu marquées que ce soit pour la lutéine ou la vitamine D. En revanche, en phase intestinale, la teneur en lutéine bioaccessible est 6 fois plus importante pour le biscuit que pour la crème après 240 minutes de digestion. La teneur en vitamine D bioaccessible tend à l'inverse à êtremoins élevée pour le biscuit que pour les deux autres matrices en phase intestinale.Conclusion: Les résultats de digestion in vitrodynamique montrent que la structure des aliments module la cinétique de digestion des lipides et de l’amidon, et consécutivement la cinétique de libération des micronutriments
Latest Advances in Targeting the Tumor Microenvironment for Tumor Suppression
No full textThe tumor bulk is composed of a highly heterogeneous population of cancer cells, as well as a large variety of resident and infiltrating host cells, extracellular matrix proteins, and secreted proteins, collectively known as the tumor microenvironment (TME). The TME is essential for driving tumor development by promoting cancer cell survival, migration, metastasis, chemoresistance, and the ability to evade the immune system responses. Therapeutically targeting tumor-associated macrophages (TAMs), cancer-associated fibroblasts (CAFs), regulatory T-cells (T-regs), and mesenchymal stromal/stem cells (MSCs) is likely to have an impact in cancer treatment.
In this review, we focus on describing the normal physiological functions of each of these cell types and their behavior in the cancer setting. Relying on the specific surface markers and secreted molecules in this context, we review the potential targeting of these cells inducing their depletion, reprogramming, or di erentiation, or inhibiting their pro-tumor functions or recruitment. Di erent approaches were developed for this targeting, namely, immunotherapies, vaccines, small interfering RNA, or small molecules
