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The segmentation of medical and dental images is a fundamental step in automated clinical decision support systems. It supports the entire clinical workflow from diagnosis, therapy planning, intervention, and follow-up. In this paper, we propose a novel tool to accurately process a full-face segmentation in about 5 minutes that would otherwise require an average of 7h of manual work by experienced clinicians. This work focuses on the integration of the state-of-the-art UNEt TRansformers (UNETR) of the Medical Open Network for Artificial Intelligence (MONAI) framework. We trained and tested our models using 618 de-identified Cone-Beam Computed Tomography (CBCT) volumetric images of the head acquired with several parameters from different centers for a generalized clinical application. Our results on a 5-fold cross-validation showed high accuracy and robustness with a Dice score up to 0.962±0.02. Our code is available on our public GitHub repository .

Pikeperch Sander lucioperca is a species mainly reared in recirculating aquaculture systems (RASs), but it remains very sensitive to stress and handling. Plant phenolic compounds such as quercetin or rutin are frequently investigated as feed additives to improve the growth and well‐being of fish reared in RAS, but their impact on pikeperch and RAS microbial communities has never been studied. Our objectives were to (i) test the effect of quercetin or rutin addition to feed (2.2 g kg −1 diet) on the growth, stress, and innate immunity of pikeperch reared in RAS and (ii) assess the consequence of those additives on the RAS water microbial communities. Pikeperch of 307 (±45) g starting weight were reared in nine experimental RAS ( n = 3) and fed for 84 days on a diet enriched or not (control treatment) with quercetin or rutin (feeding rate: 1.5%). Considering the start (T0) and the end (T84) of the experiment, we compare the fish growth, feed conversion ratio (FCR), morphoanatomical and physiological status, and the water microbial diversity and composition through a metabarcoding approach performed on the 16S rRNA gene. Whereas no effect on fish was recorded with quercetin (624.0 ± 21.9 g final weight), rutin (558.0 ± 10.7 g final weight) reduced pikeperch growth (0.54 vs. 0.69%–0.64% day −1 ), and increased FCR (1.70 vs. 1.2–1.4) compared to control (622.0 ± 16.8 g final weight) and quercetin treatments, respectively. No effect was observed on all fish physiological parameters analyzed separately, but a multifactorial analysis reveals that fish fed with rutin have a different overall physiological state. Quercetin induced a shift in the microbial community structure and composition, whereas there was no effect of treatments on microbial richness or evenness. A dietary supplementation with quercetin or rutin has no or a negative impact on pikeperch growth and physiology and modifies the microbial diversity in RAS. Effects of additives being species‐dependent, precautions must be taken when formulating feed supplements, which must be based on precise studies.

Truffles ascocarps need carbon to grow, but it is not known whether this carbon comes directly from the tree (heterotrophy) or from soil organic matter (saprotrophy). The objective of this work was to investigate the heterotrophic side of the ascocarp nutrition by assessing the allocation of carbon by the host to Tuber melanosporum mycorrhizas and ascocarps. In 2010, a single hazel tree selected for its high truffle (Tuber melanosporum) production and situated in the west part of the Vosges, France, was labeled with (13)CO2. The transfer of (13)C from the leaves to the fine roots and T. melanosporum mycorrhizas was very slow compared with the results found in the literature for herbaceous plants or other tree species. The fine roots primarily acted as a carbon conduit; they accumulated little (13)C and transferred it slowly to the mycorrhizas. The mycorrhizas first formed a carbon sink and accumulated (13)C prior to ascocarp development. Then, the mycorrhizas transferred (13)C to the ascocarps to provide constitutive carbon (1.7 mg of (13)C per day). The ascocarps accumulated host carbon until reaching complete maturity, 200 days after the first labeling and 150 days after the second labeling event. This role of the Tuber ascocarps as a carbon sink occurred several months after the end of carbon assimilation by the host and at low temperature. This finding suggests that carbon allocated to the ascocarps during winter was provided by reserve compounds stored in the wood and hydrolyzed during a period of frost. Almost all of the constitutive carbon allocated to the truffles (1% of the total carbon assimilated by the tree during the growing season) came from the host.

Dead organic matter (OM) is a major source of nitrogen (N) for plants. The majority of plants support N uptake by symbiosis with arbuscular mycorrhizal (AM) fungi. Mineralization of N is regulated by microfauna, in particular, protozoa grazing on bacteria. We hypothesized that AM fungi and protozoa interactively facilitate plant N nutrition from OM. In soil systems consisting of an OM patch and a root compartment, plant N uptake and consequences for plant carbon (C) allocation were investigated using stable isotopes. Protozoa mobilized N by consuming bacteria, and the mobilized N was translocated via AM fungi to the host plant. The presence of protozoa in both the OM and root compartment stimulated photosynthesis and the translocation of C from the host plant via AM fungi into the OM patch. This stimulated microbial activity in the OM patch, plant N uptake from OM and doubled plant growth. The results indicate that protozoa increase plant growth by both mobilization of N from OM and by protozoa-root interactions, resulting in increased C allocation to roots and into the rhizosphere, thereby increasing plant nutrient exploitation. Hence, mycorrhizal plants need to interact with protozoa to fully exploit N resources from OM.

The genetic structure of ectomycorrhizal (ECM) fungal populations results from both vegetative and sexual propagation. In this study, we have analysed the spatial genetic structure of Tuber melanosporum populations, a heterothallic ascomycete that produces edible fruit bodies. Ectomycorrhizas from oaks and hazels from two orchards were mapped and genotyped using simple sequence repeat markers and the mating type locus. The distribution of the two T. melanosporum mating types was also monitored in the soil. In one orchard, the genetic profiles of the ascocarps were compared with those of the underlying mycorrhizas. A pronounced spatial genetic structure was found. The maximum genet sizes were 2.35 and 4.70 m in the two orchards, with most manifesting a size < 1 m. Few genets persisted throughout two seasons. A nonrandom distribution pattern of the T. melanosporum was observed, resulting in field patches colonized by genets that shared the same mating types. Our findings suggest that competition occurs between genets and provide basic information on T. melanosporum propagation patterns that are relevant for the management of productive truffle orchards.

Ectomycorrhizae create a multitrophic ecosystem formed by the association between tree roots, mycelium of the ectomycorrhizal fungus, and a complex microbiome. Despite their importance in the host tree's physiology and in the functioning of the ectomycorrhizal symbiosis, detailed studies on ectomycorrhiza-associated bacterial community composition and their temporal dynamics are rare. Our objective was to investigate the composition and dynamics of Tuber melanosporum ectomycorrhiza-associated bacterial communities from summer to winter seasons in a Corylus avellana tree plantation. We used 16S ribosomal RNA (rRNA)-based pyrosequencing to compare the bacterial community structure and the richness in T. melanosporum's ectomycorrhizae with those of the bulk soil. The T. melanosporum ectomycorrhizae harbored distinct bacterial communities from those of the bulk soil, with an enrichment in Alpha- and Gamma-proteobacteria. In contrast to the bacterial communities of truffle ascocarps that vastly varies in composition and richness during the maturation of the fruiting body and to those from the bulk soil, T. melanosporum ectomycorrhiza-associated bacterial community composition stayed rather stable from September to January. Our results fit with a recent finding from the same experimental site at the same period that a continuous supply of carbohydrates and nitrogen occurs from ectomycorrhizae to the fruiting bodies during the maturation of the ascocarps. We propose that this creates a stable niche in the ectomycorrhizosphere although the phenology of the tree changes.

The National Cancer Institute Informatics Technology for Cancer Research (ITCR) program provides a series of funding mechanisms to create an ecosystem of open-source software (OSS) that serves the needs of cancer research. As the ITCR ecosystem substantially grows, it faces the challenge of the long-term sustainability of the software being developed by ITCR grantees. To address this challenge, the ITCR sustainability and industry partnership working group (SIP-WG) was convened in 2019. The charter of the SIP-WG is to investigate options to enhance the long-term sustainability of the OSS being developed by ITCR, in part by developing a collection of business model archetypes that can serve as sustainability plans for ITCR OSS development initiatives. The working group assembled models from the ITCR program, from other studies, and from the engagement of its extensive network of relationships with other organizations (eg, Chan Zuckerberg Initiative, Open Source Initiative, and Software Sustainability Institute) in support of this objective. This paper reviews the existing sustainability models and describes 10 OSS use cases disseminated by the SIP-WG and others, including 3D Slicer, Bioconductor, Cytoscape, Globus, i2b2 (Informatics for Integrating Biology and the Bedside) and tranSMART, Insight Toolkit, Linux, Observational Health Data Sciences and Informatics tools, R, and REDCap (Research Electronic Data Capture), in 10 sustainability aspects: governance, documentation, code quality, support, ecosystem collaboration, security, legal, finance, marketing, and dependency hygiene. Information available to the public reveals that all 10 OSS have effective governance, comprehensive documentation, high code quality, reliable dependency hygiene, strong user and developer support, and active marketing. These OSS include a variety of licensing models (eg, general public license version 2, general public license version 3, Berkeley Software Distribution, and Apache 3) and financial models (eg, federal research funding, industry and membership support, and commercial support). However, detailed information on ecosystem collaboration and security is not publicly provided by most OSS. We recommend 6 essential attributes for research software: alignment with unmet scientific needs, a dedicated development team, a vibrant user community, a feasible licensing model, a sustainable financial model, and effective product management. We also stress important actions to be considered in future ITCR activities that involve the discussion of the sustainability and licensing models for ITCR OSS, the establishment of a central library, the allocation of consulting resources to code quality control, ecosystem collaboration, security, and dependency hygiene.

Nickel-hyperaccumulator plants are of interest due to their potential use in agromining. We aimed to characterize leaf traits and Ni concentration variabilities occurring between individual plants, leaves of differing age or between various leaf tissues, in a single Greek population of the Ni-hyperaccumulator Leptoplax emarginata (Boiss.) O.E. Schulz. We linked these results to ecophysiological characteristics and other element concentrations at leaf and leaf tissue scales. We measured leaf gas exchanges, stomatal density, and we carried out rapid freezing and freeze-drying processes on leaf sections before microanalysis with scanning electron microscopy and energy-dispersive spectrometry. Leaf or leaf-tissue Ni concentrations were influenced by a combination of individual plant and leaf age factors. The greatest Ni concentrations were found in the highly transpiring young and thin leaves with the greatest stomatal densities. Indeed, Ni was statistically seven times more concentrated in both epidermis layers than in their bulk neighbour leaf counterparts, whatever the leaf age. In both epidermis layers, increases in the Ni–S and Mg–S correlations from the oldest leaves to the youngest ones were observed. The Mg:Ni, Ca:Ni and P:Ni mass ratios decreased from the oldest leaves to the mature leaves. We would recommend time-series characterization of leaf traits belonging to at least three plant replicates in order to take into account the allogamous character of many Ni-hyperaccumulator plants. Long-distance Ni transport via the xylem is predominant in the Ni-hyperaccumulator L. emarginata whereas a complementary redistribution via the phloem should also occur. The perspectives of this study are the validation and refinement of this process over shorter periods using relevant tracers.

Tomato plants are attacked by a variety of herbivore pests and among them, the leafminer Tuta absoluta, which is currently a major threat to global tomato production. Although the commercial tomato is susceptible to T. absoluta attacks, a better understanding of the defensive plant responses to this pest will help in defining plant resistance traits and broaden the range of agronomic levers that can be used for an effective integrated pest management strategy over the crop cycle. In this study, we developed an integrative approach combining untargeted metabolomic and transcriptomic analyses to characterize the local and systemic metabolic responses of young tomato plants to T. absoluta larvae herbivory. From metabolomic analyses, the tomato response appeared to be both local and systemic, with a local response in infested leaves being much more intense than in other parts of the plant. The main response was a massive accumulation of phenolamides with great structural diversity, including rare derivatives composed of spermine and dihydrocinnamic acids. The accumulation of this family of specialized metabolites was supported by transcriptomic data, which showed induction of both phenylpropanoid and polyamine precursor pathways. Moreover, our transcriptomic data identified two genes strongly induced by T. absoluta herbivory, that we functionally characterized as putrescine hydroxycinnamoyl transferases. They catalyze the biosynthesis of several phenolamides, among which is caffeoylputrescine. Overall, this study provided new mechanistic clues of the tomato/T. absoluta interaction.

ObjectivesWe hypothesised that patients having experienced one coronary event in their life were susceptible to present differences in their pathways of care and within 1 year of their life courses. We aimed to compare pathways between first-time ST-elevation myocardial infarction (STEMI) and STEMI with prior myocardial infarction (MI).DesignA retrospective observational study based on the Observatoire des Syndromes Coronariens Aigus du réseau RESCUe (OSCAR) registry collecting all suspected STEMI from 10 percutaneous coronary intervention centres in France.SettingAll patients with STEMI from 2013 to 2017 were included (N=6306 with 5423 first-time STEMI and 883 STEMI with prior MI). We provided a matching analysis by propensity score based on cardiovascular risk factors.ParticipantsWe defined first-time STEMI as STEMI occurring at the inclusion date, and STEMI with prior MI as STEMI with a history of MI prior to the inclusion date.ResultsPatients with first-time STEMI and patients with STEMI with prior MI were equally treated during hospitalisation and at discharge. At 12 months, patients with first-time STEMI had a lower adherence to BASIC treatment (ie, beta-blocker, antiplatelet therapy, statin and converting enzyme inhibitor) (48.11% vs 58.58%, p=0.0167), more frequently completed the cardiac rehabilitation programme (44.33% vs 31.72%, p=0.0029), more frequently changed their lifestyle behaviours; more frequently practiced daily physical activity (48.11% vs 35.82%, p=0.0043) and more frequently stopped smoking at admission (69.39% vs 55.00%, p=0.0524). The estimated mortality was higher for patients with STEMI with prior MI at 1 month (p=0.0100), 6 months (p=0.0500) and 1 year (p=0.0600).ConclusionsWe provided an exhaustive overview of the real-life clinical practice conditions of STEMI management. The patients with STEMI with prior MI presented an optimised use of prehospital resources, which was probably due to their previous experience, and showed a better adherence to drug therapy compared with patients with first-time STEMI.Trial registration numberCommission Nationale de l’Informatique et des Libertés (number 2 013 090 v0).