MRI-Based Radiomics Input for Prediction of 2-Year Disease Recurrence in Anal Squamous Cell Carcinoma

International audiencePurpose: Chemo-radiotherapy (CRT) is the standard treatment for non-metastatic anal squamous cell carcinomas (ASCC). Despite excellent results for T1-2 stages, relapses still occur in around 35% of locally advanced tumors. Recent strategies focus on treatment intensification, but could benefit from a better patient selection. Our goal was to assess the prognostic value of pre-therapeutic MRI radiomics on 2-year disease control (DC). Methods: We retrospectively selected patients with non-metastatic ASCC treated at the CHU Bordeaux and in the French FFCD0904 multicentric trial. Radiomic features were extracted from T2-weighted pre-therapeutic MRI delineated sequences. After random division between training and testing sets on a 2:1 ratio, univariate and multivariate analysis were performed on the training cohort to select optimal features. The correlation with 2-year DC was assessed using logistic regression models, with AUC and accuracy as performance gauges, and the prediction of disease-free survival using Cox regression and Kaplan-Meier analysis. Results: A total of 82 patients were randomized in the training (n = 54) and testing sets (n = 28). At 2 years, 24 patients (29%) presented relapse. In the training set, two clinical (tumor size and CRT length) and two radiomic features (FirstOrder_Entropy and GLCM_JointEnergy) were associated with disease control in univariate analysis and included in the model. The clinical model was outperformed by the mixed (clinical and radiomic) model in both the training (AUC 0.758 versus 0.825, accuracy of 75.9% versus 87%) and testing (AUC 0.714 versus 0.898, accuracy of 78.6% versus 85.7%) sets, which led to distinctive high and low risk of disease relapse groups (HR 8.60, p = 0.005). Conclusion: A mixed model with two clinical and two radiomic features was predictive of 2-year disease control after CRT and could contribute to identify high risk patients amenable to treatment intensification with view of personalized medicine

Réponse et résilience de la biodiversité d'une Forêt Tropicale après Perturbation

Forest are currently threatened by the global changing context. Maintain the goods and services they provide require clarifying tree community diversity response to disturbance, that determine forest functioning, maintenance and resilience. This is specifically crucial in tropical forests that are both the most threatened regions and those with the highest environmental, social and economic stakes. In this context, this work studies the taxonomic and functional response to disturbance of a Neotropical community. Through post-disturbance diversity trajectories in the long term we examined the ecological processes underlying community response to disturbance, explicit the taxonomic and functional aspects of community recovery, and eventually discussed some perspectives for forest management and modeling. From the monitoring dataset of the Paracou experimental station in French Guiana we examined tree community response to disturbance over the thirty years following a disturbance gradient. First, we developed and tested a diversity estimator tackling the taxonomic uncertainties of forest inventories and improving the accuracy of biodiversity surveys. The estimator based on botanical/vernacular association probability to account of taxonomic uncertainties in various diversity measurement framework. The estimator, further used in this worked, was first calibrated to improve the estimation accuracy and was then validated with real forest inventories. The results allowed designing an inventory protocol optimizing the cost of inventories and the accuracy of the diversity measure. Second, we analyzed the post-disturbance taxonomic and functional trajectories of diversity, composition and redundant at the scale of the whole community. We combined the 30 years of botanical inventories with a large functional dataset encompassing key leaf, root, wood and life-history functional traits. Eventually, we specifically analyzed the post-disturbance recruitment processes and the diversity and composition succession.We highlighted the emergence after disturbance of deterministic processes driving community taxonomic and functional response to disturbance. Deterministic processes favored the recruitment of a restricted pool of pioneer species, similar for to all communities and disturbance intensity. Around fifteen years after disturbance, the recovery of community initial characteristics started with the recovery of stochastic processes driving non-disturbed communities. At the whole-community scale, this succession translated into a cyclic trajectory of taxonomic composition leading to a recovery of the pre-disturbance composition and a maintenance of differences among communities. Disturbance increased both taxonomic richness and evenness until an intensity threshold above which, in accordance with the Intermediate Disturbance Hypothesis, the taxonomic richness decreased and the pioneers became persistently dominant. The functional trajectories however proved decoupled from taxonomic trajectories. Functional diversity increased whatever the disturbance, without any intensity threshold, and functional composition trajectories converged in the functional space without marked differences among communities. This decoupling was explained by the functional redundancy that mitigated the functional impact of disturbance and proved to be the slow parameter of tropical forest recovery.Our results showed a tangible taxonomic and functional recovery of communities after the gradient of disturbance but this recovery proved decades-long. In the light of those results, we discussed the practices of sustainable forest management and several perspectives of forest diversity modeling.Dans le contexte de changements actuel, clarifier la réponse des forêts aux perturbations est indispensable pour préserver les biens et services qu’elles rendent. Le fonctionnement et le maintien des forêts dépend largement de la diversité des communautés d'arbres qui devient un enjeu majeur, en particulier dans les régions tropicales où les forêts sont les plus menacées et où les enjeux économiques, sociaux et environnementaux sont les plus importants. Cette thèse étudie la réponse aux perturbations de la diversité taxonomique et fonctionnelle d’une communauté en forêt Néotropicale. Nous analysons les trajectoires de diversité sur le long terme pour déterminer les processus écologiques sous-jacents la réponse des communautés aux perturbations, à expliciter les aspects taxonomiques et fonctionnels de la restauration, et enfin à discuter de perspectives de gestion et de modélisation de la dynamique forestière. Le dispositif expérimental de Paracou en Guyane Française a permis de suivre la réponse des communautés d'arbres sur 30 années après un gradient de perturbation. Dans un premier temps, nous avons établi et validé un estimateur de diversité fiable, pour pallier les incertitudes de botaniques des inventaires forestiers et des bases de données fonctionnelles. L'estimateur propage les incertitudes taxonomiques aux mesures de diversité via les probabilités d'associations entre noms vernaculaires et noms botaniques. L’estimateur de diversité, employé dans l'ensemble de la thèse, a été calibré pour optimiser l'estimation la précision de l'estimation en fonction des données disponibles, puis testé avec des inventaires forestiers pré-exploitation pour proposer un protocole d'inventaire optimisant le coût et la précision de ces inventaires. Dans un deuxième temps, en combinant les inventaires botaniques à un large jeu de données fonctionnel comprenant des traits des feuilles, du bois et des traits d'histoire de vie, nous avons analysé les trajectoires de diversité, de composition, et de redondance taxonomique et fonctionnelle des communautés après perturbation . Enfin, nous avons spécifiquement étudié les trajectoires de diversité et de composition des communautés recrutées. Notre étude a montré l'émergence de processus déterministes après perturbation déterminant la réponse taxonomique et fonctionnelle des communautés en favorisant le recrutement d'un pool restreint de pionnières. Nous avons montré la restauration progressive des communautés pré-perturbation et de processus stochastiques tels qu'observés en l'absence de perturbation. Les perturbations ont augmenté la richesse et l'équitabilité taxonomiques des communautés jusqu'à un certain seuil, au delà duquel la dominance de quelques pionnières diminue la richesse taxonomique, conformément à la théorie des perturbations intermédiaires. Les trajectoires fonctionnelles en revanche ont montré une augmentation de la diversité quelle que soit la perturbation et une convergences fonctionnelle entre les communautés: ce découplage entre trajectoires taxonomiques et fonctionnelles s'est expliqué par la redondance fonctionnelle des communautés, atténuant l’impact fonctionnel des perturbations. Nos résultats ont montré une restauration taxonomique et fonctionnelle tangible des communautés mais encore inachevée. A la lumière de ces résultats nous proposons une discussion sur la possibilité d'une exploitation durable des forêts et de nouvelles perspectives de modélisation de la diversité

FiguresData.xlsx

Data table for figures."Increasing atmospheric dryness reduces boreal forest tree growth"How trees respond to increasing atmospheric dryness has important implications for forest growth. Here, the authors use a network of tree-ring records to quantify the multidecadal impact of vapour pressure deficit trends on boreal forests in Canada.</p

Biodiversity Response and Resilience to Disturbance of a Tropical Forest

Dans le contexte de changements actuel, clarifier la réponse des forêts aux perturbations est indispensable pour préserver les biens et services qu’elles rendent. Le fonctionnement et le maintien des forêts dépend largement de la diversité des communautés d'arbres qui devient un enjeu majeur, en particulier dans les régions tropicales où les forêts sont les plus menacées et où les enjeux économiques, sociaux et environnementaux sont les plus importants. Cette thèse étudie la réponse aux perturbations de la diversité taxonomique et fonctionnelle d’une communauté en forêt Néotropicale. Nous analysons les trajectoires de diversité sur le long terme pour déterminer les processus écologiques sous-jacents la réponse des communautés aux perturbations, à expliciter les aspects taxonomiques et fonctionnels de la restauration, et enfin à discuter de perspectives de gestion et de modélisation de la dynamique forestière. Le dispositif expérimental de Paracou en Guyane Française a permis de suivre la réponse des communautés d'arbres sur 30 années après un gradient de perturbation. Dans un premier temps, nous avons établi et validé un estimateur de diversité fiable, pour pallier les incertitudes de botaniques des inventaires forestiers et des bases de données fonctionnelles. L'estimateur propage les incertitudes taxonomiques aux mesures de diversité via les probabilités d'associations entre noms vernaculaires et noms botaniques. L’estimateur de diversité, employé dans l'ensemble de la thèse, a été calibré pour optimiser l'estimation la précision de l'estimation en fonction des données disponibles, puis testé avec des inventaires forestiers pré-exploitation pour proposer un protocole d'inventaire optimisant le coût et la précision de ces inventaires. Dans un deuxième temps, en combinant les inventaires botaniques à un large jeu de données fonctionnel comprenant des traits des feuilles, du bois et des traits d'histoire de vie, nous avons analysé les trajectoires de diversité, de composition, et de redondance taxonomique et fonctionnelle des communautés après perturbation . Enfin, nous avons spécifiquement étudié les trajectoires de diversité et de composition des communautés recrutées. Notre étude a montré l'émergence de processus déterministes après perturbation déterminant la réponse taxonomique et fonctionnelle des communautés en favorisant le recrutement d'un pool restreint de pionnières. Nous avons montré la restauration progressive des communautés pré-perturbation et de processus stochastiques tels qu'observés en l'absence de perturbation. Les perturbations ont augmenté la richesse et l'équitabilité taxonomiques des communautés jusqu'à un certain seuil, au delà duquel la dominance de quelques pionnières diminue la richesse taxonomique, conformément à la théorie des perturbations intermédiaires. Les trajectoires fonctionnelles en revanche ont montré une augmentation de la diversité quelle que soit la perturbation et une convergences fonctionnelle entre les communautés: ce découplage entre trajectoires taxonomiques et fonctionnelles s'est expliqué par la redondance fonctionnelle des communautés, atténuant l’impact fonctionnel des perturbations. Nos résultats ont montré une restauration taxonomique et fonctionnelle tangible des communautés mais encore inachevée. A la lumière de ces résultats nous proposons une discussion sur la possibilité d'une exploitation durable des forêts et de nouvelles perspectives de modélisation de la diversité.Forest are currently threatened by the global changing context. Maintain the goods and services they provide require clarifying tree community diversity response to disturbance, that determine forest functioning, maintenance and resilience. This is specifically crucial in tropical forests that are both the most threatened regions and those with the highest environmental, social and economic stakes. In this context, this work studies the taxonomic and functional response to disturbance of a Neotropical community. Through post-disturbance diversity trajectories in the long term we examined the ecological processes underlying community response to disturbance, explicit the taxonomic and functional aspects of community recovery, and eventually discussed some perspectives for forest management and modeling. From the monitoring dataset of the Paracou experimental station in French Guiana we examined tree community response to disturbance over the thirty years following a disturbance gradient. First, we developed and tested a diversity estimator tackling the taxonomic uncertainties of forest inventories and improving the accuracy of biodiversity surveys. The estimator based on botanical/vernacular association probability to account of taxonomic uncertainties in various diversity measurement framework. The estimator, further used in this worked, was first calibrated to improve the estimation accuracy and was then validated with real forest inventories. The results allowed designing an inventory protocol optimizing the cost of inventories and the accuracy of the diversity measure. Second, we analyzed the post-disturbance taxonomic and functional trajectories of diversity, composition and redundant at the scale of the whole community. We combined the 30 years of botanical inventories with a large functional dataset encompassing key leaf, root, wood and life-history functional traits. Eventually, we specifically analyzed the post-disturbance recruitment processes and the diversity and composition succession.We highlighted the emergence after disturbance of deterministic processes driving community taxonomic and functional response to disturbance. Deterministic processes favored the recruitment of a restricted pool of pioneer species, similar for to all communities and disturbance intensity. Around fifteen years after disturbance, the recovery of community initial characteristics started with the recovery of stochastic processes driving non-disturbed communities. At the whole-community scale, this succession translated into a cyclic trajectory of taxonomic composition leading to a recovery of the pre-disturbance composition and a maintenance of differences among communities. Disturbance increased both taxonomic richness and evenness until an intensity threshold above which, in accordance with the Intermediate Disturbance Hypothesis, the taxonomic richness decreased and the pioneers became persistently dominant. The functional trajectories however proved decoupled from taxonomic trajectories. Functional diversity increased whatever the disturbance, without any intensity threshold, and functional composition trajectories converged in the functional space without marked differences among communities. This decoupling was explained by the functional redundancy that mitigated the functional impact of disturbance and proved to be the slow parameter of tropical forest recovery.Our results showed a tangible taxonomic and functional recovery of communities after the gradient of disturbance but this recovery proved decades-long. In the light of those results, we discussed the practices of sustainable forest management and several perspectives of forest diversity modeling

30 Years of postdisturbance recruitment in a Neotropical forest

International audienceQuestions: Long-term community response to disturbance can follow manifold successional pathways depending on the interplay between various recruitment processes. Analyzing the succession of recruited communities provides a long-term perspective on forest response to disturbance. Specifically, postdisturbance recruitment trajectories assess (a) the successive phases of postdisturbance response and the role of deterministic recruitment processes, and (b) the return to predisturbance state of recruits taxonomic/functional diversity/composition.Location: Amazonian rainforest, Paracou station, French Guiana.Methods: We analyzed trajectories of recruited tree communities, from twelve forest plots of 6.25 ha each, during 30 years following a disturbance gradient that ranged from 10% to 60% of aboveground biomass removed. We measured recruited community taxonomic composition turnover, compared to whole predisturbance community, and assessed their functional composition by measuring the community weighted means for seven leaf, stem, and life-history functional traits. We also measured recruited community taxonomic richness, taxonomic evenness, and functional diversity and compared them to the diversity values from a random recruitment process.Results; While control plots trajectories resembled random recruitment trajectories, postdisturbance trajectories diverged significantly. This divergence corresponded to an enhanced recruitment of light-demanding species that became dominant above a disturbance intensity threshold. After breakpoints in time, though, recruitment trajectories returned to diversity values and composition similar to those of predisturbance and control plots community.Conclusions: Following disturbance, recruitment processes specific to undisturbed community were first replaced by the emergence of more restricted, deterministic recruitment processes favoring species with efficient light use and acquisition. Then, a second phase corresponded to a decades-long recovery of recruits predisturbance taxonomic and functional diversity and composition that remained unachieved after 30 years

Estimation of the number of tree species in French Guiana by extropolation of permanent plots richness

International audienc

Increasing atmospheric dryness reduces boreal forest tree growth

Abstract Rising atmospheric vapour pressure deficit (VPD) associated with climate change affects boreal forest growth via stomatal closure and soil dryness. However, the relationship between VPD and forest growth depends on the climatic context. Here we assess Canadian boreal forest responses to VPD changes from 1951-2018 using a well-replicated tree-growth increment network with approximately 5,000 species-site combinations. Of the 3,559 successful growth models, we observed a relationship between growth and concurrent summer VPD in one-third of the species-site combinations, and between growth and prior summer VPD in almost half of those combinations. The relationship between previous year VPD and current year growth was almost exclusively negative, while current year VPD also tended to reduce growth. Tree species, age, annual temperature, and soil moisture primarily determined tree VPD responses. Younger trees and species like white spruce and Douglas fir exhibited higher VPD sensitivity, as did areas with high annual temperature and low soil moisture. Since 1951, summer VPD increases in Canada have paralleled tree growth decreases, particularly in spruce species. Accelerating atmospheric dryness in the decades ahead will impair carbon storage and societal-economic services

Beyond species richness and biomass: Impact of selective logging and silvicultural treatments on the functional composition of a neotropical forest

International audienceTropical forests harbor the greatest terrestrial biodiversity and provide various ecosystem services. The increase of human activities on these forests, among which logging, makes the conservation of biodiversity and associated services strongly dependent on the sustainability of these activities. However the indicators commonly used to assess the impact of forest exploitation, namely species richness and biomass, provide a limited understanding of their sustainability. Here, we assessed the sustainability of common forest exploitation in the Guiana Shield studying the recovery of two ecosystem services i.e. carbon storage and wood stock, and an ecosystem function i.e. seed dispersal by animals. Specifically, we compared total and commercial biomass, as well as functional composition in seed size of animal-dispersed species in replicated forest plots before and 27 years after exploitation. Species richness is also studied to allow comparison. While species richness was not affected by forest exploitation, total and commercial biomass as well as seed size of animal-dispersed species decreased 27 years after exploitation, similarly to forests affected by hunting. These results show that ecosystem services and function likely did not recover even at the lowest intensity of forest exploitation studied, questioning the sustainability of the most common rotation-cycle duration applied in the tropics

Variation of daily sapflux density of 22 trees during a dry season within an Amazonian rainforest

This data file contains the climate data (daily rain in mm, daily potential evapotranspiration - PET - in mm, and relative soil water content - RSWC) and tree sapflux density data (daily sapflux density, Ds, in kg dm-2 day-1) used in Maréchaux et al. All methods, units and tree codes are explicitely described and provided in the corresponding paper