Detecting anomalous behaviors in multivariate systems using machine learning

Aircrafts are complex systems that are generating more and more data. An Airbus A320 equipped with FOMAX (Flight Operations and MAintenance eXchanger) records 24000 parameters and a Pratt & Whitney PW1000G GTF engine incorporates 5000 sensors, leading to terabytes of data being recorded for each flight. Modernization of military aircrafts and usage of Unmanned Aerial Vehicle (UAV) fleets also lead to large quantity of data. Detecting anomalies in those systems is valuable as a warning system to detect unexpected behaviors, faulty systems to be replaced or even discard readings of faulty sensors

Boosting Institute of Chemistry, Technology and Metallurgy in water biomonitoring - BIOLAWEB

Project "Boosting Institute of Chemistry, Technology and Metallurgy in Water Biomonitoring" (BIOLAWEB) aims to strengthen the research and innovation capacity of the Institute of Chemistry, Technology and Metallurgy, National Institute of the Republic of Serbia, University of Belgrade (UB-ICTM) in biodiversity assessment and biomonitoring. UB-ICTM researchers made a noticeable contribution to the study of biodiversity, community ecology, and conservation of water bodies in South-Eastern Europe. However, a knowledge on index development and intercalibration following the EU standards for lakes and watercourse monitoring is still lacking in this geographic region. Similarly, there is a knowledge gap in DNA-based ecological status assessment in SEE.Abstract from ExcellMater Conference 2024 (ExcellMater Conference 2024: Innovative biomaterials for novel medical devices) published in Supplementary Issue

Differential global distribution of marine picocyanobacteria gene clusters reveals distinct niche-related adaptive strategies

The ever-increasing number of available microbial genomes and metagenomes provides new opportunities to investigate the links between niche partitioning and genome evolution in the ocean, especially for the abundant and ubiquitous marine picocyanobacteria Prochlorococcus and Synechococcus. Here, by combining metagenome analyses of the Tara Oceans dataset with comparative genomics, including phyletic patterns and genomic context of individual genes from 256 reference genomes, we show that picocyanobacterial communities thriving in different niches possess distinct gene repertoires. We also identify clusters of adjacent genes that display specific distribution patterns in the field (eCAGs) and are thus potentially involved in the same metabolic pathway and may have a key role in niche adaptation. Several eCAGs are likely involved in the uptake or incorporation of complex organic forms of nutrients, such as guanidine, cyanate, cyanide, pyrimidine, or phosphonates, which might be either directly used by cells, for example for the biosynthesis of proteins or DNA, or degraded to inorganic nitrogen and/or phosphorus forms. We also highlight the enrichment of eCAGs involved in polysaccharide capsule biosynthesis in Synechococcus populations thriving in both nitrogen- and phosphorus-depleted areas vs. low-iron (Fe) regions, suggesting that the complexes they encode may be too energy-consuming for picocyanobacteria thriving in the latter areas. In contrast, Prochlorococcus populations thriving in Fe-depleted areas specifically possess an alternative respiratory terminal oxidase, potentially involved in the reduction of Fe(III) to Fe(II). Altogether, this study provides insights into how phytoplankton communities populate oceanic ecosystems, which is relevant to understanding their capacity to respond to ongoing climate change

Differential global distribution of marine picocyanobacteria gene clusters reveals distinct niche-related adaptive strategies

The ever-increasing number of available microbial genomes and metagenomes provides new opportunities to investigate the links between niche partitioning and genome evolution in the ocean, especially for the abundant and ubiquitous marine picocyanobacteria Prochlorococcus and Synechococcus. Here, by combining metagenome analyses of the Tara Oceans dataset with comparative genomics, including phyletic patterns and genomic context of individual genes from 256 reference genomes, we show that picocyanobacterial communities thriving in different niches possess distinct gene repertoires. We also identify clusters of adjacent genes that display specific distribution patterns in the field (eCAGs) and are thus potentially involved in the same metabolic pathway and may have a key role in niche adaptation. Several eCAGs are likely involved in the uptake or incorporation of complex organic forms of nutrients, such as guanidine, cyanate, cyanide, pyrimidine, or phosphonates, which might be either directly used by cells, for example for the biosynthesis of proteins or DNA, or degraded to inorganic nitrogen and/or phosphorus forms. We also highlight the enrichment of eCAGs involved in polysaccharide capsule biosynthesis in Synechococcus populations thriving in both nitrogen- and phosphorus-depleted areas vs. low-iron (Fe) regions, suggesting that the complexes they encode may be too energy-consuming for picocyanobacteria thriving in the latter areas. In contrast, Prochlorococcus populations thriving in Fe-depleted areas specifically possess an alternative respiratory terminal oxidase, potentially involved in the reduction of Fe(III) to Fe(II). Altogether, this study provides insights into how phytoplankton communities populate oceanic ecosystems, which is relevant to understanding their capacity to respond to ongoing climate change

Association between convalescent plasma treatment and mortality in COVID-19: a collaborative systematic review and meta-analysis of randomized clinical trials.

Funder: laura and john arnold foundationBACKGROUND: Convalescent plasma has been widely used to treat COVID-19 and is under investigation in numerous randomized clinical trials, but results are publicly available only for a small number of trials. The objective of this study was to assess the benefits of convalescent plasma treatment compared to placebo or no treatment and all-cause mortality in patients with COVID-19, using data from all available randomized clinical trials, including unpublished and ongoing trials (Open Science Framework, https://doi.org/10.17605/OSF.IO/GEHFX ). METHODS: In this collaborative systematic review and meta-analysis, clinical trial registries (ClinicalTrials.gov, WHO International Clinical Trials Registry Platform), the Cochrane COVID-19 register, the LOVE database, and PubMed were searched until April 8, 2021. Investigators of trials registered by March 1, 2021, without published results were contacted via email. Eligible were ongoing, discontinued and completed randomized clinical trials that compared convalescent plasma with placebo or no treatment in COVID-19 patients, regardless of setting or treatment schedule. Aggregated mortality data were extracted from publications or provided by investigators of unpublished trials and combined using the Hartung-Knapp-Sidik-Jonkman random effects model. We investigated the contribution of unpublished trials to the overall evidence. RESULTS: A total of 16,477 patients were included in 33 trials (20 unpublished with 3190 patients, 13 published with 13,287 patients). 32 trials enrolled only hospitalized patients (including 3 with only intensive care unit patients). Risk of bias was low for 29/33 trials. Of 8495 patients who received convalescent plasma, 1997 died (23%), and of 7982 control patients, 1952 died (24%). The combined risk ratio for all-cause mortality was 0.97 (95% confidence interval: 0.92; 1.02) with between-study heterogeneity not beyond chance (I2 = 0%). The RECOVERY trial had 69.8% and the unpublished evidence 25.3% of the weight in the meta-analysis. CONCLUSIONS: Convalescent plasma treatment of patients with COVID-19 did not reduce all-cause mortality. These results provide strong evidence that convalescent plasma treatment for patients with COVID-19 should not be used outside of randomized trials. Evidence synthesis from collaborations among trial investigators can inform both evidence generation and evidence application in patient care

La vulnérabilité des lacs face au couplage du climat et des perturbations anthropiques locales : approche paléolimnologique basée sur les cladocères

Lake ecosystems are increasingly subjected to multiple perturbations but their response is too rarely considered in overall. But, though a complex set of interactions, each perturbation can modulate the intensity of the impact of each other on lakes, and thus their response. In this context, this work is focused on deepening our understanding of the response of lakes in a context of multiples perturbations, over the long-term. We studied this response performing a paleolimnological approach (based on cladoceran) on three large, deep lakes (Lakes Geneva, Bourget and Annecy) submitted to a similar regional perturbation (i.e., climate warming) and varying intensities of two local perturbations (i.e., changes in nutrient inputs and fisheries managment practices). The ability of cladoceran to integrate the temporal changes in the pelagic food web in response to three environmental perturbations makes them a suitable model to reconstruct changes in the whole pelagic community. Specifically, we addressed (i) changes in cladoceran communities, during the last century, in response to three environmental perturbations and (ii) the impact of these perturbations on reproductive behavior of Daphnia. However, the lack of knowledge in large, deep lakes on the representativity of source cladoceran communitites by fossil assemblages in sediments firstly led to a methodological calibration. This last showed that the represention level of source communities was different according to the type of remain. Parthenogenetic remain assemblages (i.e., exoskeleton) reflect accurately the taxonomical and size structure of source communities in contrast to ephippia which are reliable proxy to reconstruct reproductive behavior. Following these results, the paleolimnological reconstructions of cladoceran communities showed that their ecological trajectories are controlled by complex interactions between the three perturbations, according to time periods and lakes. Moreover, the response of cladoceran communties to climate was different between the three lakes as a function of the intensity of local forcings. These observations suggest that it is important to include the role of local perturbations in predicting the future impact of climate change on lakes. The impact of environmental perturbations on the reproductive behavior of Daphnia is such that interspecific hybridization events were observed. However, these hybridization events were the result of different sensitivity to perturbations among Daphnia species.Les écosystèmes lacustres sont de plus en plus soumis à de multiples perturbations mais leur réponse est encore trop rarement considérée de façon globale. En effet, au travers d'un jeu d'interactions complexes, chaque perturbation peut moduler l'intensité de l'impact des autres sur les lacs, et de ce fait, leur réponse. Dans ce contexte, ce travail doctoral est axé sur l'approfondissement de notre compréhension de la réponse des lacs à un contexte de perturbations multiples, sur le long terme. Pour cela, trois grands lacs profonds (le lac Léman, du Bourget et d'Annecy), soumis à une perturbation régionale similaire (i.e., le réchauffement climatique) et à deux perturbations locales (i.e., les changements dans le statut trophique et dans les pratiques de gestion piscicole) d'intensités différentes, ont été choisis. La réponse de ces lacs à ces changements a été abordée au travers d'une approche paléolimnologique, basée sur les cladocères. En effet, la capacité de ceux-ci à intégrer les changements temporels dans le réseau trophique pélagique en réponse aux trois perturbations environnementales en fait un modèle adéquat pour reconstruire les changements à l'échelle de la communauté pélagique. Plus précisément, nous avons abordé (i) les changements dans les communautés de cladocères, au cours du siècle dernier, en réponse aux trois perturbations environnementales et (ii) l'impact de ces perturbations sur les stratégies de reproduction des Daphnies. Cependant, le manque de connaissance dans les grands lacs profonds sur la représentativité des communautés sources de cladocères par les assemblages de restes archivés dans les sédiments a tout d'abord conduit à faire un point méthodologique. Ce dernier a abouti à la mise en évidence de différences dans le niveau de représentation de communautés sources de cladocères selon le type de restes utilisés. La composition taxonomique et la structure en taille des restes parthénogénétiques (i.e., exosquelettes) reflètent relativement bien celle des communautés sources. Quant aux éphippies (œufs de dormance), elles se révèlent des indicateurs fiables pour reconstruire les comportements de reproduction. Suite à ces résultats, les reconstructions paléolimnologiques des communautés de cladocères montrent que leur trajectoire écologique était contrôlée par des interactions complexes entre les trois pertubations différentes, selon les périodes de temps et entre les lacs. De plus, la réponse des communautés de cladocères au climat était différente entre les trois lacs comme une fonction de l'intensité des forçages locaux. Ces observations suggèrent qu'il est important d'inclure le rôle des perturbations locales dans la prédiction de l'impact futur des changements climatiques sur les lacs. L'impact des perturbations environnementales sur le comportement de reproduction des Daphnies est tel que des évènements d'hybridation interspécifique ont été observés. Cependant, ces évènements d'hybridation sont issus de sensibilité aux trois perturbations environnementales différentes entre les espèces de Daphnies

The vulnerability of lakes face to the coupling of climate and local disturbance : paleolimnological approach based on cladocerans

Les écosystèmes lacustres sont de plus en plus soumis à de multiples perturbations mais leur réponse est encore trop rarement considérée de façon globale. En effet, au travers d'un jeu d'interactions complexes, chaque perturbation peut moduler l'intensité de l'impact des autres sur les lacs, et de ce fait, leur réponse. Dans ce contexte, ce travail doctoral est axé sur l'approfondissement de notre compréhension de la réponse des lacs à un contexte de perturbations multiples, sur le long terme. Pour cela, trois grands lacs profonds (le lac Léman, du Bourget et d'Annecy), soumis à une perturbation régionale similaire (i.e., le réchauffement climatique) et à deux perturbations locales (i.e., les changements dans le statut trophique et dans les pratiques de gestion piscicole) d'intensités différentes, ont été choisis. La réponse de ces lacs à ces changements a été abordée au travers d'une approche paléolimnologique, basée sur les cladocères. En effet, la capacité de ceux-ci à intégrer les changements temporels dans le réseau trophique pélagique en réponse aux trois perturbations environnementales en fait un modèle adéquat pour reconstruire les changements à l'échelle de la communauté pélagique. Plus précisément, nous avons abordé (i) les changements dans les communautés de cladocères, au cours du siècle dernier, en réponse aux trois perturbations environnementales et (ii) l'impact de ces perturbations sur les stratégies de reproduction des Daphnies. Cependant, le manque de connaissance dans les grands lacs profonds sur la représentativité des communautés sources de cladocères par les assemblages de restes archivés dans les sédiments a tout d'abord conduit à faire un point méthodologique. Ce dernier a abouti à la mise en évidence de différences dans le niveau de représentation de communautés sources de cladocères selon le type de restes utilisés. La composition taxonomique et la structure en taille des restes parthénogénétiques (i.e., exosquelettes) reflètent relativement bien celle des communautés sources. Quant aux éphippies (œufs de dormance), elles se révèlent des indicateurs fiables pour reconstruire les comportements de reproduction. Suite à ces résultats, les reconstructions paléolimnologiques des communautés de cladocères montrent que leur trajectoire écologique était contrôlée par des interactions complexes entre les trois pertubations différentes, selon les périodes de temps et entre les lacs. De plus, la réponse des communautés de cladocères au climat était différente entre les trois lacs comme une fonction de l'intensité des forçages locaux. Ces observations suggèrent qu'il est important d'inclure le rôle des perturbations locales dans la prédiction de l'impact futur des changements climatiques sur les lacs. L'impact des perturbations environnementales sur le comportement de reproduction des Daphnies est tel que des évènements d'hybridation interspécifique ont été observés. Cependant, ces évènements d'hybridation sont issus de sensibilité aux trois perturbations environnementales différentes entre les espèces de Daphnies.Lake ecosystems are increasingly subjected to multiple perturbations but their response is too rarely considered in overall. But, though a complex set of interactions, each perturbation can modulate the intensity of the impact of each other on lakes, and thus their response. In this context, this work is focused on deepening our understanding of the response of lakes in a context of multiples perturbations, over the long-term. We studied this response performing a paleolimnological approach (based on cladoceran) on three large, deep lakes (Lakes Geneva, Bourget and Annecy) submitted to a similar regional perturbation (i.e., climate warming) and varying intensities of two local perturbations (i.e., changes in nutrient inputs and fisheries managment practices). The ability of cladoceran to integrate the temporal changes in the pelagic food web in response to three environmental perturbations makes them a suitable model to reconstruct changes in the whole pelagic community. Specifically, we addressed (i) changes in cladoceran communities, during the last century, in response to three environmental perturbations and (ii) the impact of these perturbations on reproductive behavior of Daphnia. However, the lack of knowledge in large, deep lakes on the representativity of source cladoceran communitites by fossil assemblages in sediments firstly led to a methodological calibration. This last showed that the represention level of source communities was different according to the type of remain. Parthenogenetic remain assemblages (i.e., exoskeleton) reflect accurately the taxonomical and size structure of source communities in contrast to ephippia which are reliable proxy to reconstruct reproductive behavior. Following these results, the paleolimnological reconstructions of cladoceran communities showed that their ecological trajectories are controlled by complex interactions between the three perturbations, according to time periods and lakes. Moreover, the response of cladoceran communties to climate was different between the three lakes as a function of the intensity of local forcings. These observations suggest that it is important to include the role of local perturbations in predicting the future impact of climate change on lakes. The impact of environmental perturbations on the reproductive behavior of Daphnia is such that interspecific hybridization events were observed. However, these hybridization events were the result of different sensitivity to perturbations among Daphnia species