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Surplus bread fermentation by Pleurotus ostreatus monitored by magnetic resonance imaging
No full textInternational audienceThis study addresses circular approaches to reuse food surpluses and losses, focusing on starchy products like bread that are fermented by fungi to produce a nutrient-rich biomass. Traditional methods have evaluated fungal growth at a macro scale, but improving the processing of heterogeneous substrates, such as highly porous ones, requires detailed insight into local fungal activity and growth. Magnetic Resonance Imaging (MRI) offers a unique advantage by simultaneously capturing morphological details and water distribution. The present work aimed to assess MRI as a non-destructive, non-invasive tool for monitoring spatial and temporal changes in biomass during solid-state fermentation (SSF) of bread slices with Pleurotus ostreatus. MRI protocols were developed to measure morphological changes and map transverse NMR relaxation times. MRI data were validated against conventional measurements of water content and dry matter, with further evaluation through fibre and protein analyses to determine added nutritional value.Bread was shown to be a suitable substrate for cultivating fungi, producing a nutritionally-valuable biomass rich in soluble fibre and changes in some amino acid composition. T 2 relaxation was an effective focus to monitor mycelial growth through association to mycelial hydrolysis and water content distribution. T 2 mapping revealed significant heterogeneities in the bread, which persisted long under experimental conditions employed (approximatively one month). While the observed changes were at the macroscopic level, future microscale investigations using multi-exponential T 2 could help isolate fungal signals and enable quantitative biomass assessment.</p
Francis Hallé (1938–2025), founder of the study of tree architecture
No full textInternational audienceFrancis Hallé (1938-2025) was one of the most influential French botanists of the last century. He founded plant architectural analysis, showing that post-embryogenic development follows intrinsic, species-specific rules, and that the immense diversity of tree forms can be captured by a finite set of recurring architectural models. He also co-invented the Radeau des Cimes, a canopy-access platform that transformed tropical forest research by making the canopy directly observable and sampleable, and by catalysing ambitious, multinational expeditions. Beyond research, Hallé was an extraordinary communicator: through books, drawings, and public talks, he fought plant blindness and taught generations to look at plants differently. In his final years, he led a major project with the aim to recreate a large, primary forest in Western Europe. Hallé died on 31 December 2025, leaving a scientific, cultural, and ecological legacy that will long outlive him
RAC: Retrieval-Augmented Clarification for Faithful Conversational Search
No full textInternational audienceClarification questions help conversational search systems resolve ambiguous or underspecified user queries. While prior work has focused on fluency and alignment with user intent, especially through facet extraction, much less attention has been paid to grounding clarifications in the underlying corpus. Without such grounding, systems risk asking questions that cannot be answered from the available documents. We introduce RAC (Retrieval-Augmented Clarification), a framework for generating corpus-faithful clarification questions. After comparing several indexing strategies for retrieval, we fine-tune a large language model to make optimal use of research context and to encourage the generation of evidence-based question. We then apply contrastive preference optimization to favor questions supported by retrieved passages over ungrounded alternatives. Evaluated on four benchmarks, RAC demonstrate significant improvements over baselines. In addition to LLM-as-Judge assessments, we introduce novel metrics derived from NLI and data-to-text to assess how well questions are anchored in the context, and we demonstrate that our approach consistently enhances faithfulness
Revealing the diversity of collective experimentation in agriculture: Constructing idealtypes from French case studies
No full textInternational audienceContext: The agroecological transition underscores the need to rethink knowledge production in agriculture, especially in relation to experimentation. This includes involving a wider range of stakeholders and exploring diverse and complementary forms of experimentation. Objective: This article aims to shed light on the diversity of existing collective experimentations, in order to document the ongoing renewal of experimental approaches and to propose benchmarks for understanding and supporting them. Methods: We conducted 34 semi-structured interviews and 10 observant participations, leading to the identification of 28 case studies that we define as collective experimentations. We define collective experimentation as the process of implementing and monitoring an intervention with uncertain outcomes, which leads to the production of knowledge. We did a comprehensive analysis of these collective experimentations, to understand how and why they are conducted. To do so, our analysis considered both the physical design of the experimental setups and the questions addressed, as well as the collective organization of the actors involved. Results and Conclusions: We propose six idealtypes of collective experimentations: Idealtype A: Replicating experimental situations to generate standardized data, Idealtype B: Integrating data from diverse experimental practices in a joint analysis, Idealtype C: Distributing questions to generate knowledge on a common topic, Idealtype D: Pooling a diversity of experiences to explore a common subject, Idealtype E: Distributing activities within a single experimental situation and Idealtype F: Gathering human and material resources on a single site to experiment jointly on several experimental situations. Significance: These idealtypes shed light on the diversity of collective experimentation approaches in agriculture, which are often under described in the literature. By offering a set of structured reference points, it can support researchers, facilitators, and practitioners in recognizing, designing and valuing collective experimentations adapted to their contexts. It opens new perspectives for rethinking how experimental knowledge is produced, shared, and valued to support agroecological transitions
Letter to the Editor: Comment on the recent article titled “Diagnostic and economic evaluation of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry with machine learning for screening of Johne's disease from dairy cow serum”
No full textInternational audienceWe read with great interest the recent article evaluating MALDI-TOF MS combined with machine learning for Johne's disease screening (Sarkar et al., 2026). Although the study is innovative, we believe that both the diagnostic and economic assessments rely on assumptions that substantially undermine the validity of the conclusions.From a methodological standpoint, the diagnostic evaluation suffers from several weaknesses: the limited sample size associated with the risk of overfitting when applying machine learning to complex proteomic profiles, and the lack of clarity on animal selection, which raises concerns about representativeness relative to the intended clinical context. Moreover, the study reports only relative sensitivity (Se) and specificity (Sp) of MALDI-TOF compared with the ELISA, not to the true infection status.Despite this, the economic model assumes absolute Se and Sp of 80% and 83% for MALDI-TOF, and 50% and 99% for the ELISA. These assumptions concerning the MALDI-TOF are unjustified. Given that the MALDI-TOF Se and Sp are only relative to ELISA, its true Se and Sp should-at best-be the product of both: approximately 0.8 × 0.5 = 40% for Se and 0.83 × 0.99 ≈ 82% for Sp. Even this computation presumes that the 27% MALDI-TOF "false positives" are indeed false, and not animals misclassified by the imperfect ELISA reference.</p
Bis(monoacylglycero)phosphate protects murine RAW 264.7 macrophages against 7-Ketocholesterol-induced apoptosis and impaired autophagy
No full textInternational audienceAtherosclerosis, a leading cause of cardiovascular disease, is driven by the accumulation of oxidized low-density lipoproteins (oxLDL) in arterial walls. 7-Ketocholesterol (7KC), a major oxysterol found in oxLDL and atherosclerotic plaques, triggers multiple cell injuries including loss of lysosomal integrity, oxidative stress, apoptosis, and impaired autophagy in vascular cells. Bis(monoacylglycero)phosphate (BMP), also known as lysobisphosphatidic acid, is a unique phospholipid concentrated in the endolysosomal compartment, known to regulate vesicle dynamics, lysosomal enzyme activities, intracellular cholesterol trafficking and its oxidative metabolism. Using a validated model of BMP enrichment in murine RAW 264.7 macrophages, we investigated whether BMP could exert protective activity against 7KC-induced damage. Our findings revealed that BMP enrichment provides comprehensive protection against 7KC at the cellular level by preserving cell viability, morphology, and neutral lipid balance. Mechanistically, BMP enrichment prevented apoptosis by maintaining mitochondrial integrity and blocking caspase activation. This was demonstrated by normalized BAX/BCL2 ratios, preserved pro-Caspase-3 levels, and reduced PARP cleavage. Remarkably, BMP enrichment also restored autophagic flux, thereby preventing the pathological accumulation of LC3-II and p62 that characterizes autophagy dysfunction. Enhanced colocalization between LC3 and BMP suggests direct functional interactions in the stress response. Gene expression analysis confirmed that BMP enrichment normalized the transcriptional dysregulation of key autophagy regulators, including Sqstm1, Becn1, and Pink1. Taken together, these results suggest that BMP is an endogenous protective factor that counteracts 7KC-induced cellular damage at multiple steps by regulating cell death and autophagy pathways in a coordinated manner
Defeated major resistance loci may act as Trojan horses compromising resistance pyramiding in grapevine
No full textInternational audienceResistance breeding offers invaluable perspectives for environment-friendly crop protection, but its success may be limited by the breakdown of plant resistance by pathogen strains. With the breeding and use of varieties carrying multiple genetic resistances, grapevine (Vitis spp.) represents a distinctive model for perennials to investigate the agreement that pyramiding broadens and enhances the efficacy and durability of resistance. To this end, grapevine progenies segregating for four major resistance loci against Plasmopara viticola (Rpvs) were used to evaluate single and pyramided loci when confronted with naive and Rpv-breaking pathogen strains. In pyramiding, undefeated and defeated Rpvs provided either beneficial, neutral, or detrimental quantitative effects, depending on the loci combination and pathogen strain. In particular, the fact that defeated loci may compromise resistance highlighted important implications for the breeding of perennials. Thorough phenotypic investigations of pyramiding schemes emerge as a critical step for the effective and durable management of genetic resistances
Impact of a well-defined indigenous starter on microbial communities and technological properties of raw milk during backslopping practice
No full textInternational audienceBackslopping, which involves using the whey from a previous batch as a starter for a new production run, is one of the oldest traditional cheese-making methods and is still widely used today. However, this technique can sometimes lead to acidification failures, necessitating the use of industrial starters to quickly restart production and minimise economic loss. This study investigated the effect of using a well-defined indigenous starter culture on raw milk during backslopping. The microbial composition and technological characteristics of successive subcultures were analyzed during one month of backslopping with and without the starter added. The results showed that the indigenous starter remained highly stable in skim milk, predominantly drove homolactic fermentation. The raw milk alone displayed greater initial microbial diversity and metabolic variability but then stabilised and Lactococcus lactis became dominant from day four onwards of backslopping. The combination of the indigenous starter with the raw milk, rapidly established L. lactis dominance, directing the ecosystem towards homolactic fermentation from the start of backslopping. The addition of the indigenous starter impacted particularly subdominant populations and technological properties, resulting in an acidification that met the requirements of the Rocamadour PDO from the start of the backslopping. From day fifteen onwards, comparison of bacterial communities with and without the starter added became differentiated, demonstrating that adding the indigenous starter reduced variability in bacterial composition. Notably, coexistence between the indigenous starter and the raw milk flora was observed, suggesting that this could be a promising option for farmer producers to strengthen the link between the product and its microbial terroir
A 7-year multi-criteria analysis of sugarcane intercropping compared to conventional cropping systems
No full textInternational audienceAbstractLong-term studies are crucial for evaluating how intercropping affects the agronomic, environmental, and socio-economic sustainability of sugarcane systems. Intercropping with cover crops is expected to improve soil fertility and reduce herbicide use; however, its long-term effects on yield, weed dynamics, and production costs remain unclear, particularly under tropical conditions. Weed pressure has been hypothesized to drive yield decline over time, yet the temporal evolution of weed communities and their consequences for system sustainability remain poorly understood. We hypothesized that intercropping would modify ecosystem functions and services by increasing weed diversity and soil fertility, reducing herbicide use, and also increasing labor and production costs. To test this hypothesis, we conducted the first 7-year field experiment on Reunion Island, comparing four sugarcane intercropping systems with conventional chemical and low weed control systems. A multi-criteria approach assessed weed community dynamics, soil fertility, sugarcane yield and quality, herbicide use, labor, and economic performance over a complete crop cycle, including multiple ratoons. We show that weed pressure increased over time in both chemical and intercropping systems due to greater weed cover and species richness. Weed community structure differed during the first 3 years but later homogenized under sugarcane dominance. This increase led to more manual weeding in intercropping systems and to increased herbicide use in chemical ones, resulting in a 61% reduction in herbicide use under intercropping. After 7 years, soil chemical and biological fertility remained unchanged, while physical fertility improved with companion crop and weed development. Sugarcane yield and sucrose content were maintained, but production costs and working hours increased. This study demonstrates that sugarcane intercropping reduces herbicide dependence without compromising yield, though at higher labor costs. Systems maintaining spontaneous flora in inter-rows appear to offer a promising compromise for sustainable weed management. Further research on this system should be conducted in different pedoclimatic conditions
Federate cross-disciplinary work on the effects of pesticides on all aspects of health (human, animal, environmental)
No full textPlant protection products used in agriculture contain molecules specifically designed to be toxic to target organisms. However, their use can also have unintended effects, posing potential risks to ecosystems and non-target organisms, including humans. Research has deepened our understanding of the links between exposure to these substances and the effects observed in the environment. In particular, studies have highlighted how even low levels of exposure can cause chronic effects on non-target organisms and disrupt ecosystems. These findings underscore the importance of quantifying and characterising these exposures in order to better assess their potential impacts on human health and the environment.International audienceAs part of the Ecophyto II+ plan, now known as the Ecophyto 2030 strategy, research projects have been funded to increase knowledge about exposure to plant protection products (PPPs) and their impacts on health and the environment. These studies have led to the development of methodologies for pesticide monitoring and improved risk assessment. We provide a synthesis of the results of these projects and a discussion of key issues-risk assessment, regulation, and collective responsibility-to inform public policy and promote sustainable agricultural practices. Future perspectives include the assessment of chemical interactions in the context of climate change. An interdisciplinary approach and collaboration between researchers, health professionals, farmers, the agro-industry, and public authorities are essential to reduce the risks associated with pesticide use