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In the last few years, the study of environmental DNA (eDNA) has drawn attention for many reasons, including its advantages for monitoring and conservation purposes. So far, in aquatic environments, most of eDNA research has focused on the detection of single species using species-specific markers. Recently, species inventories based on the analysis of a single generalist marker targeting a larger taxonomic group (eDNA metabarcoding) have proven useful for bony fish and amphibian biodiversity surveys. This approach involves in situ filtering of large volumes of water followed by amplification and sequencing of a short discriminative fragment from the 12S rDNA mitochondrial gene. In this study, we went one step further by investigating the spatial representativeness (i.e. ecological reliability and signal variability in space) of eDNA metabarcoding for large-scale fish biodiversity assessment in a freshwater system including lentic and lotic environments. We tested the ability of this approach to characterize large-scale organization of fish communities along a longitudinal gradient, from a lake to the outflowing river. First, our results confirm that eDNA metabarcoding is more efficient than a single traditional sampling campaign to detect species presence, especially in rivers. Second, the species list obtained using this approach is comparable to the one obtained when cumulating all traditional sampling sessions since 1995 and 1988 for the lake and the river, respectively. In conclusion, eDNA metabarcoding gives a faithful description of local fish biodiversity in the study system, more specifically within a range of a few kilometers along the river in our study conditions, i.e. longer than a traditional fish sampling site.

The management of lakes requires the definition of physico-chemical thresholds to be used for ecosystem preservation or restoration. According to the European Water Framework Directive, the limits between physico-chemical quality classes must be set consistently with biological quality elements. One way to do this consists in analyzing the response of aquatic communities to environmental gradients across monitoring sites and in identifying ecological community thresholds, i.e. zones in the gradients where the species turnover is the highest. In this study, fish data from 196 lakes in France were considered to derive ecological thresholds using the multivariate method of gradient forest. The analysis was performed on 25 species and 36 environmental parameters. The results revealed the highest importance of maximal water temperature in the distribution of fish species. Other important parameters included geographical factors, dissolved organic carbon concentration and water transparency, while nutrients appeared to have low influence. In spite of the diversity of species responses to the gradients, community thresholds were detected in the gradients of the most important physico-chemical parameters and of total phosphorus and nitrate concentrations as well. The thresholds identified in such macroecological study may highlight new patterns of species natural distribution and improve niche characterization. Moreover, when factors that may be influenced by human activities are involved, the thresholds could be used to set environmental standards for lake preservation. La gestion des plans d'eau nécessite la définition de seuils physico-chimiques pour la préservation ou la restauration des écosystèmes. Selon la Directive Cadre européenne sur l'Eau, les limites de classes de qualité physico-chimiques doivent être fixées en cohérence avec les éléments de qualité biologique. Une façon de faire consiste à analyser les réponses des communautés aquatiques aux gradients environnementaux formés par les sites de monitoring et d'identifier des seuils écologiques de communautés, c'est-à-dire des zones dans les gradients où le turnover des espèces est le plus important. Dans cette étude, les données de pêches provenant de 196 plans d'eau ont été considérées pour rechercher des seuils écologiques avec la méthode de gradient forest. L'analyse a porté sur 25 espèces avec 36 paramètres environnementaux. Les résultats ont révélé que la température maximale était le facteur le plus important dans la distribution des espèces de poissons. Les autres paramètres importants étaient les facteurs géographiques, la concentration en carbone organique dissous et la transparence de l'eau alors que les nutriments semblaient avoir peu d'influence. Malgré la diversité de réponses des espèces aux gradients, des seuils de communautés ont été détectés dans les gradients des paramètres physico-chimiques les plus importants ainsi que dans ceux des concentrations en phosphore total et en nitrates. Les seuils identifiés dans une telle étude macroécologique peuvent faire apparaître de nouveaux patrons de distribution naturelle des poissons et améliorer la caractérisation des niches spécifiques. De plus, quand des facteurs influencés par les activités humaines sont impliqués, ces seuils pourraient être utilisés pour fixer des limites pour la protection des plans d'eau.

Environmental DNA (eDNA) metabarcoding is revolutionizing the monitoring of aquatic biodiversity. The use of eDNA has the potential to enable non-invasive, cost-effective, time-efficient and high-sensitivity monitoring of fish assemblages. Although the capacity of eDNA metabarcoding to describe fish assemblages is recognised, research efforts are still needed to better assess the spatial and temporal variability of the eDNA signal and to ultimately design an optimal sampling strategy for eDNA monitoring. In this context, we sampled three different lakes (a dam reservoir, a shallow eutrophic lake and a deep oligotrophic lake) every 6 weeks for 1 year. We performed four types of sampling for each lake (integrative sampling of sub-surface water along transects on the left shore, the right shore and above the deepest zone, and point sampling in deeper layers near the lake bottom) to explore the spatial variability of the eDNA signal at the lake scale over a period of 1 year. A metabarcoding approach was applied to analyse the 92 eDNA samples in order to obtain fish species inventories which were compared with traditional fish monitoring methods (standardized gillnet samplings). Several species known to be present in these lakes were only detected by eDNA, confirming the higher sensitivity of this technique in comparison with gillnetting. The eDNA signal varied spatially, with shoreline samples being richer in species than the other samples. Furthermore, deep-water samplings appeared to be non-relevant for regularly mixed lakes, where the eDNA signal was homogeneously distributed. These results also demonstrate a clear temporal variability of the eDNA signal that seems to be related to species phenology, with most of the species detected in spring during the spawning period on shores, but also a peak of detection in winter for salmonid and coregonid species during their reproduction period. These results contribute to our understanding of the spatio-temporal distribution of eDNA in lakes and allow us to provide methodological recommendations regarding where and when to sample eDNA for fish monitoring in lakes.

Sexual selection is considered the major cause of sexual dimorphism, but recent observations suggest that natural selection may play a more important role in the evolution of sex differentiation than previously recognized. Therefore, studying the trade-offs between natural selection and sexual selection is crucial to a better understanding of the ecology underlying the evolution of sexual dimorphism. The freshwater blenny Salaria fluviatilis, a fish inhabiting lakes and rivers around the Mediterranean Sea, displays strong sexual dimorphism in size, shape, and behavior (i.e., larger body and head size for males and higher swimming requirements for females during the reproductive period). We tested for differences in sexual dimorphism in size and shape between the populations from lake and river habitats with the goal of identifying the trade-offs between natural and sexual selection that underlie variations in sexual dimorphism in this species. Our results show i) differences in sexual size dimorphism (SSizeD) in accordance to Rensch's rule (i.e., larger individuals in rivers associated with higher SSizeD), and ii) a decrease in shape differentiation between males and females in lake populations. Together, this suggests that the different environmental conditions between lake and river habitats (e.g., resource limitations, predation pressure, water velocity) affect the relative importance of sexual selection in the display of sexual dimorphism within the species. This study highlights the importance of considering the environmental conditions to which populations are exposed to better understand the ecology underlying the evolution of sexual dimorphism.

The research reported and discussed in this thesis represents a novel approach to User Interface evaluation and optimisation through cognitive modelling. This is achieved through the development and testing of a toolkit or platform titled Toolkit for Optimisation of Interface System Evolution (TOISE). The research is conducted in two main phases. In phase 1, the Adaptive Control of Thought Rational (ACT-R) cognitive architecture is used to design Simulated Users (SU) models. This allows models of user interaction to be tested on a specific User Interface (UI). In phase 2, an evolutionary algorithm is added and used to evolve and test an optimised solution to User Interface layout based on the original interface design. The thesis presents a technical background, followed by an overview of some applications in their respective fields. The core concepts behind TOISE are introduced through a discussion of the Adaptive Control of Thought – Rational (ACT-R) architecture with a focus on the ACT-R models that are used to simulate users. The notion of adding a Genetic Algorithm optimiser is introduced and discussed in terms of the feasibility of using simulated users as the basis for automated evaluation to optimise usability. The design and implementation of TOISE is presented and discussed followed by a series of experiments that evaluate the TOISE system. While the research had to address and solve a large number of technical problems the resulting system does demonstrate potential as a platform for automated evaluation and optimisation of user interface layouts. The limitations of the system and the approach are discussed and further work is presented. It is concluded that the research is novel and shows considerable promise in terms of feasibility and potential for optimising layout for enhanced usability.

Quantify changes in workload in relation to the anatomic pathologist workforce. In house pathology reports for cytology and surgical specimens from a regional hospital laboratory over a nine- year period (2011-2019) were analyzed, using custom computer code. Report length for the diagnosis+microscopic+synoptic report, number of blocks, billing classification (L86x codes), billings, national workload model (L4E 2018), regional workload model (W2Q), case count, and pathologist workforce in full-time equivalents (FTEs) were quantified. Randomly selected cases (n = 1,100) were audited to assess accuracy. The study period had 574,093 pathology reports that could be analyzed. The coding accuracy was estimated at 95%. From 2011 to 2019: cases/year decreased 6% (66,056 to 61,962), blocks/year increased 20% (236,197 to 283,751), L4E workload units increased 23% (165,276 to 203,894), W2Q workload units increased 21% (149,841 to 181,321), report lines increased 19% (606,862 to 723,175), workforce increased 1% (30.42 to 30.77 FTEs), billings increased 13% ( $6,766,927 to $ 7,677,109). W2Q in relation to L4E underweights work in practices with large specimens by up to a factor of 2x. Work by L4E for large specimens is underrated by W2Q. Reporting requirements and pathology work-up have increased workload per pathology case. Work overall has increased significantly without a commensurate workforce increase. The significant practice changes in the pathology work environment should prompt local investment in the anatomic pathology workforce.

The scent of roses (Rosa x hybrida) is composed of hundreds of volatile molecules.Monoterpenes represent up to 70% percent of the scent content in some cultivars, such asthe Papa Meilland rose. Monoterpene biosynthesis in plants relies on plastid-localizedterpene synthases. Combining transcriptomic and genetic approaches, we show thatthe Nudix hydrolase RhNUDX1, localized in the cytoplasm, is part of a pathway for thebiosynthesis of free monoterpene alcohols that contribute to fragrance in roses. TheRhNUDX1 protein shows geranyl diphosphate diphosphohydrolase activity in vitro andsupports geraniol biosynthesis in planta.

Assess the work environment of salaried pathologists via (1) the national workload system (L4E), (2) work distribution among/in three hospital groups, and (3) the frequency of significant absences or departures (SADs). Automated analysis of pathology reports from a regional laboratory (accessioned 2011-2019) using validated computer code. The study set contained 574,099 pathology reports, reported by 63 pathologists. The average yearly L4E workload units/full-time equivalent for three hospital groups were 8,101.6, 6,906.5 and 4,215.8. The average Gini coefficient for full-time pathologists in the three hospital groups were respectively 0.05, 0.16 and 0.23. The average yearly SADs rates were respectively 13%, 16% and 9%. The group with the highest SADs rate had the intermediate Gini coefficient and intermediate workload. High individual workload and work maldistribution appear to be associated with SADs. Individual workload maximums and greater transparency may be essential for limiting staff turnover, maintaining high morale, and efficient laboratory function with a high quality of care.

PurposeFDG PET/CT is emerging as a new tool for the evaluation of acute encephalitis (AE). However, to date, there are no exclusively pediatric studies on the use of FDG PET for suspected AE. The objective of this study was to compare qualitative and quantitative brain PET to conventional brain imaging in a cohort of children, and to identify patterns of metabolic abnormalities characteristic of AE.MethodsThis retrospective study included 34 children imaged with PET/CT, CT and magnetic resonance imaging (MRI). The positivity rate of all three imaging modalities was measured. Besides visual assessment, quantification of relative regional brain metabolism (RRBM) was performed and compared to a database of normal pediatric brains.ResultsFourteen subjects had a clinical diagnosis of autoimmune encephalitis (AIE) or encephalitis of unknown origin (EX), six of anti-N-methyl-D-aspartate receptor (anti-NMDAr) encephalitis, three of Hashimoto’s encephalopathy, three of neurolupus and eight had other subtypes of encephalitis.Quantitative PET was abnormal in 100% of cases, visually assessed PET in 94.1% of subjects, MRI in 41.2% and CT in 6.9%. RRBM quantification demonstrated multiple hyper and hypo metabolic cortical regions in 82.3% of subjects, exclusively hypermetabolic abnormalities in 3%, and exclusively hypometabolic abnormalities in 14.7%. The basal ganglia were hypermetabolic in 26.5% of cases on visual assessment and in 58.8% of subjects using quantification.ConclusionIn our pediatric population FDG PET was more sensitive than conventional imaging for the detection of AE, and basal ganglia hypermetabolism was frequently encountered.

Background Malaria remains one of the main causes of morbidity and mortality in Cameroon. To inform vector control intervention decision making, malaria vector surveillance was conducted monthly from October 2018 to September 2020 in five selected sentinel sites (Gounougou and Simatou in the North, and Bonabéri, Mangoum and Nyabessang in the South). Methods Human landing catches (HLCs), U.S. Centers for Disease Control and Prevention (CDC) light traps, and pyrethrum spray catches (PSCs) were used to assess vector density, species composition, human biting rate (HBR), endophagic index, indoor resting density (IRD), parity, sporozoite infection rates, entomological inoculation rate (EIR), and Anopheles vectorial capacity. Results A total of 139,322 Anopheles mosquitoes from 18 species (or 21 including identified sub-species) were collected across all sites. Out of the 18 species, 12 were malaria vectors including Anopheles gambiae sensu lato (s.l.), Anopheles funestus s.l.., Anopheles nili , Anopheles moucheti , Anopheles paludis , Anopheles demeilloni , Anopheles. pharoensis , Anopheles ziemanni , Anopheles multicinctus , Anopheles tenebrosus , Anopheles rufipes , and Anopheles marshallii . Anopheles gambiae s.l. remains the major malaria vector (71% of the total Anopheles ) collected, though An. moucheti and An. paludis had the highest sporozoite rates in Nyabessang. The mean indoor HBR of Anopheles ranged from 11.0 bites/human/night (b/h/n) in Bonabéri to 104.0 b/h/n in Simatou, while outdoors, it varied from 24.2 b/h/n in Mangoum to 98.7 b/h/n in Simatou. Anopheles gambiae s.l . and An. moucheti were actively biting until at least 8:00 a.m. The mean Anopheles IRD was 17.1 females/room, and the parity rate was 68.9%. The mean EIRs for each site were 55.4 infective bites/human/month (ib/h/m) in Gounougou, 99.0 ib/h/m in Simatou, 51.2 ib/h/m in Mangoum, 24.4 ib/h/m in Nyabessang, and 18.1 ib/h/m in Bonabéri. Anopheles gambiae s.l. was confirmed as the main malaria vector with the highest vectorial capacity in all sites based on sporozoite rate, except in Nyabessang. Conclusion These findings highlight the high malaria transmission occurring in Cameroon and will support the National Malaria Control Program to design evidence-based malaria vector control strategies, and deployment of effective and integrated vector control interventions to reduce malaria transmission and burden in Cameroon, where several Anopheles species could potentially maintain year-round transmission.